I used to love RTS games, but found recently that they've gotten too complex and fiddly for my tastes. Wondering what the RTS mavens here on GOG would recommend from the catalogue.
A quick rundown of likes/dislikes:
Warcraft: Loved I and II, found III got a little too fussy with a gajillion units and special powers.
Starcraft: Pretty much perfect. Again, a bit too much with the "every unit has eight special abilities" stuff on the upper levels.
Total Annihilation: Generally good, but the "shoot across 16 screens" units piss me off no end. There also seems to be an easy "defend, amass, go forth and smash" strategy that makes the game easy once you get over that first hump in every level.
Dawn of War: Nearly perfect; my system strains to run Winter Assault, though, and I really really really hate the limited zoom out (although I understand the design reasons behind it). The special units and unique powers are, again, a bit much for me to track.
Evil Genius: As much a sim as an RTS, I guess, but I loved it.
Freedom Force: As an old-school comic geek, this was tons of fun. A bit easy, but engaging.
Dune II: My all-time classic favourite RTS, but too dated to play now, alas.
Important things for me:
*Pausing. I like to be able to pause the game and issue commands; I like to play the games relatively fast with pause/order rather than play an unpausable game slowly to keep up with an AI that can issue 12 orders simultaneously.
*Simplicity. I don't need 30 unit types with 10 unique powers each. I'm interested in having my archers/riflemen/blasters outmaneuver and flank the enemy's units, not positioning my Super Golem to unleash an Omega Charge to trigger the Nurgle Blaster that activates the Alpha Beam to power up the Grunty Tankj to fire a Floop Laser.
*Fun theme. I'd rather have slime monsters fighting space aliens than Generic Red Guys fighting Generic Green Guys. I know it's just cosmetics, but I like getting into the funky theme of a game.
*Good AI. I hate online RTS playing for a variety of reasons, but largely because I kind of suck. Seriously. I'm an old man with a slow brain. StarCraft online was like six layers of hell, because it consisted entirely of me getting my butt handed to me by 14-year-olds in Korea. I like playing the computer.
*Short levels. I'm married, and my wife seems to have some strong opinions about me disappearing for four-hour levels. I know I can save and reload, but smaller maps and quick skirmishes are more enjoyable for me than massive, sprawling, plodding games.
*Customizability. This is pretty optional, and runs a bit counter to "simplicity," above, but I like a game where I can opt to increase unit cost to increase armour, or drop firepower for additional speed, etc. I much prefer to alter unit fundamentals than deal with 100 types of units.
What do you think, GOG? Is there an RTS that's right for me?

Well apart from the last 2 points I'd probably suggest Ground Control but I seem to recall the later levels being a bit of an endurance test.
Spellforce Platinum might be worth looking at. Its a hybrid RPG/RTS but focussing more on the RTS, the RPG part is mostly your main character and select few heroes levelling up and some conversations, quests & equipment upgrades. The meat of the game is a warcraftish RTS (but better) where you do have a decent variety of units and some scope for upgrading them (though it is mostly the give unit better armour or special power rather than real customisation)

Mmm-hmmm. Not an easy one, with all the criteria you have; in fact, I'm not even sure there is a GOG that fulfills them all.
My best guess is Empire Earth Gold. It's a simple, old-school RTS, there is pausing, the AI is remarkably good, and, using the civ builder+units' own improvements, you can customize it pretty well.
However, it doesn't have a "funky" theme, but a real-history/sci-fi one. Also, it can get a bit long, but there are options to make a match shorter (p.e. playing a Deathmatch game on a tiny map against one enemy).
If you're interested, I've written a review for it.

Is The Guild an RTS? I don't care I'm reccomending it.
The Guild.

Hmm I'm also finding it tricky to match your list - generally pause and order issuing only tends to appear in the more complex RTS games, either the ones where you command very large armies, empire sims (Civilisation and Imperium Galactica 2 - though these are often turnbased games) and tactical RTS, rather like Dawn of War 2 where you have limited units.
Spellforce came to my mind also as a fun and filling RTS game with some neat quirks leaning toward RPG elements (leveling up for your avatar and learning spells and skiills as well as inventory).
Sacrifice you might also find a fun change, its a very different RTS to topdown playing, but matches tend to be shorter and faster than in Spellforce. It does lack basebuilding, though holding key manapoints is a must and you play 3rdperson (hovering camera behind the player) rather than topdown.
Edit - totally forgot, but look out for Command and Conquer the First Decade in shops - more traditional RTS and some really fun games in there from Red Alert through to the more modern games like Generals. (theres even a FPS game hiding in there for a change of pace)

Oh, no, I'm too late, I wanted to say that whatever TheJoe says, DO NOT get the Guild! While it is a great game, it is 100% incompatible with a limited timeframe. It's one of those games which you just can't play for a bit of time.

Some suggestions:
- The Kohan series (fantastic)
- Earth 2150
- Sword of the Stars (strategy level is turn based, tactical battles are pausable real-time, you can customize ships with different sections - one of my favorite strategy games)
- Total War series (same as above)
- Spellforce Platinum (it has big maps and it's not pausable, and it's kind of slow too, but epic and fun)
- Take Command: 2nd Manassas (American Civil War game; it's not funky, but it's very well implemented, and the AI is great)
EDIT: I second Sacrifice. I have the feeling you might like it.

OP, I personally love "fiddly" and ponderously slow games (Empire Earth and Medieval are personal favorites), but I think I know what you're going for. You seem to be into combat/war, action-y RTSs and RPG/RTS hybrids.
Have you played Commandoes 3, Freedom Force vs the Third Reich (sequel), Jagged Alliance 1,2?
Also, if you have a Nintendo DS or GBA, buy all the Advance Wars games, I think you'll love them. Meets all your criteria. Time-playable levels for adults, deep without a million units, lots of strategy.
Best!
P.S. I loooove Total War, but it's not playable in a wife + job timeframe.

@Wolfox and cioran
To me, it seems Shepherd asked for suggestions for a game from the GOG catalogue.
Still, maybe he will appreciate your suggestions.

Gah can't belive I forgot it -
pausable whilst still issuing orders
few unit types, but units being customisable
shorter maps (they are not too long in general though completingmight take longer if you want to keep all your men alive at the end of the fight)
Decent ai
No aliens as such, but you get USA vs USSR in the past! (fear the mountain mankilling cats)
Original War! And its on Gog too

LOL, fair point. Still, quite a few of them (Jagged Alliance 1,2) are.
Personally, OP, I hate Sacrifice, but you might like it, that's really the only other RTS on GOG in the ballpark of your likes/dislikes. It was generally well-reviewed, despite my misgivings. Try the demo first, though. It plays substantially differently than most RTS games,
Incidentally, I believe you can download the Commandoes games for free now.

I highly recommend Stronghold Crusader. Its a breath of fresh air compared to most fps games. I wrote a review on here for it, so you should look it up if you want more details. I think it fits with most of your requirements, though if you don't like medieval themes than it might not be your cup of tea. Don't be fooled though, its not corny fantasy medieval though, but rather a more historically accurate representations. I too don't have much time to game, so the crusader trail mode is great. Basically a bunch of set up skirmishes with different maps and ai opponents. The computer isn't always the smartest, but each character has different strategies to figure out so its almost like a puzzle to find their weaknesses. At least give the demo a try!

Try out Empires Dawn of the Modern World. GOG doesn't carry it but I'm sure you could pick it up for a song at Amazon.
Warlords 3 is a really good game, RTS meets RPG. Plus it is on GOG.

Not sure if this would count?
Sid Meier's Gettysburg
I played the demo way back when, seemed like a great concept for a game, and was a bit different. Far more emphasis on tactics and strategy.

I recommend Hostile Waters: Antaeus Rising. Here's a Let's Play thread that you can refer to:
http://www.gog.com/en/forum/general/would_you_guys_be_interested_in_doing_an_lp/_/1/search/hostile%20waters
Why do I recommend it? Well, it seems to fit your criteria, for the most part:
- Pausing includes pausing on the go, and auto-pausing in the war room (strategy portion of the game)
- Simplicity (less than 10 types of units)
- Fun theme (not going to spoil the story, but you'll fight more than just war machines. Also, crushable humans)
- Ok it doesn't fit the "good AI" criteria. The pathfinding AI is pretty shitty, but it's forgiveable since you can set individual unit waypoints easily, and the game has auto-pause when you are in the war room
- Short levels, check
- Customizability, CHECK CHECK CHECK!
The only thing is, you'll have to get down and dirty into the fray most of the time, but planning also plays a very important role. I would say this game definitely meets your criteria.