I tried to say it all in a short title but probably failed. I'm in the mood to play a game where I can really customise a character from the start. The customisation should offer may real choices. By real choices I mean there should be many ways to design a good build and there should not be a lot of useless or dead-end stats (e.g. stats that are only used on quest 35746B or stats that it's only worth putting a point or two in, etc).

Any suggestions? I'd give bonus points for games where the character creation options actually make intuitive sense (e.g. you can guess the sort of effects each stat will have on your character without arcane knowledge of a particular version of a a particular rule book).

Daggerfall can give you the option of giving weaknesses to your character such as being more susceptible to poison, paralisis, etc.

I'm quite sure Neverwinter Nights 2 have a large selection of choices especially if you combine multiple classes, perhaps even more if you add a combination of the right mods.

I'm thinking IceWind Dale - you get a party of 6 to roll yourself at the start!

Im incredibly biased so I'll go ahead and suggest the best rpg that I know of: Fallout 1 (and 2).
I always liked the SPECIAL stats, skills and traits system of the game. There are very few (if any really) redundant/one-use skills in the game.

Neverwinter nights 1 and 2 both have very deep character development. You can combine several different classes and prestige classes and on top of that there are mannny different spells and skills. NWN is tricky though from this point of view because it is easy to create a verrry weak character by levelling poorly and focussing on the wrong skills and attributes. Luckily there are character builders online where you can plan characters beforehand. For instance for my current playyhrough I am busy building a sorcerer/paladin/red dragon disciple character.

Heh, I know you're talking about RPG's here, but I can't help it.

Crusader Kings 2 can do exactly what you are describing, with the ruler designer dlc.

It's more of a grand strategy/rpg game, but I must confess this level of customization impressed me more than most pure RPG's I played.

Arcanum has an interesting and fun character editor, don't know if it's exactly what you are looking for. I remember a game where you made you're character based on desicions you make. Don't rembember what the name was but it was similar to how they did it in fallout 3.

I sure liked Fallout, but the SPECIAL stats seemed underdeveloped to me... I always felt like I had to take gifted+what ever causes the least trouble...

As much as I want to help the OP find something, the fact is this is just a GREAT game discussion thread period. I'm not even joking when I say I'm going to sit back and start taking notes from this. :D

1) Definitely, the Witcher games, if you haven't played them. I thought the skill tree in TW2 was really well thought-out, and it was possible to build a strong version of Geralt regardless of which skills were applied; one of my gripes with RPGs is that non-warrior builds always feel a bit nerfed.

But alchemy Geralt was just as badass and deadly as Swordsman Geralt, and that's awesome.

2) Valdis Story also qualifies, it has a good number of builds for each character that you can play (4 in total).

Here's what the skill tree looks like for one of the characters-

http://valdisstory.wikia.com/wiki/Wyatt_Skill_Tree

You can also go full on demon or angle depending on what you like. Personally, I am making him into a neutral mage/swordsman.

3) Divinity II also had awesome, and many ways to build your character, dragon form and creature; this game went all out:

http://divinity.wikia.com/wiki/Divinity_II_Skills

4) Arcanum has so, so many choices for character builds, but I never finished playing my non-combat oriented debutante Elvish lady because the game is not easy on the eyes for me. Regardless, there are many ways to build your character, play the game, and use your skills accordingly,

http://www.terra-arcanum.com/sierra/game/game-skills.html

5) Smugglers V is also cool because you can choose different character types, like bounty hunter, trader, and fleet officer etc, and then have ways to build them. I've only played as a trader so far, so I don't know how different fleet officer will be from trader, for example.

You might also want to keep your eye out for Divinity Original Sin- there are many and awesome character builds, like shadowblade and witch, and then ways to build them. There's also a feature where the dialogue options you choose determine non-combat related characteristics of the two characters, which was a pleasant surprise as I've never seen that before.

edit:

Games you might want to stay away from include Skyrim, Dragon Commander and Long Live the Queen.

I love Skyrim, but it's true that your initial skills end up being unused as soon as you get more powerful stuff, and the same happens in Dragon Commander as well; if you're looking for a fun, easy RTS with choice/consequence type gameplay, DC is definitely cool for that.

LLtQ has the worst "skill development" because the game scenarios have a habit of pigeonholing you into certain builds to play the game and finish it; to be fair, this game is not about character building anyways, but more about exploring the story..in linear ways, though there are alternative linear paths which you can take.

Regarding part of the OP's post, Titan Quest had a lot of useless dead end stats. Entire trees that if you took them, as soon as the game started getting harder you realized you had to start the whole damn thing over.

And did anyone ever really embrace poison dagger in Diablo 2?! Oh it looked cool at the beginning but as soon as you leveled up just once you could manage something a little heavier than a goddamn dirk and so of course you moved on.

XD I tend to get emotional about this.

I did have RPGs in mind but I'll allow others if they're good examples of what I asked for! :D

In Titan Quest I couldn't help but feel like the game is more about "tuning" your character and than watch how that works out, rather than having an active build.

O yes I always take gifted with fast shot. However for my next playthrough( god help me if that day ever comes ) I'll go for gifted and the charmer trait. Blistering Barnacles, i've got to figure out how to freeze time :P

Oh yes and I do apologize but seeing as this is a 'suggest a game' thread I am obliged to make a suggestion irregardless of the OP's request. Its the best game ever made, based on the best scifi film ever made (except for 2001 space odyssee...perhaps), with one of the best soundtracks ever composed. What makes it even more unique is that we'll all get to experience the game first hand in 5 years! ...Bladerunner...

So sorry, its like a reflex over which I have no control, and triggered each time somebody asks for a game suggestion...

Wizardry 6/7 has deep and complex but functional character creation, I would also recommend Daggerfall and the Realms of Arkania series but those games have too many features that are interesting in theory but aren't quite as functional (and sometimes not functional at all) in-game.
The beauty of Wizardry 6/7 is that you can sit down and logically plan out your character builds and things generally work the way they're described in the manual. As with most comparable RPGs you still kinda need meta knowledge, meaning that no matter how well you plan out your characters you might run into a wall many dozens hours into the game (happened to me). This could be seen as a hassle from a modern RPG point of view but the whole sandbox simulation aspect of grinding and experimenting and failing with your character builds and starting over with different builds is what makes these games so replayable. You can switch classes multiple times while you're playing which is a major feature of the game but not 100% necessary if you know what you're doing - intuition alone probably won't be enough for most people, I'm fairly sure I'll use a strategy guide next time I tackle this game with the intent of actually finishing it.

PS: I hear it's perfectly possible to beat the game without resorting to cheesy 'super builds' (as in Diablo 2) but some of the harder bosses are near impossible without having some prior knowledge.