Before I go into the classes I picked and why, I want to go into the general class mechanics.
In olden times a character's class really defined what their mechanical effects were. Originally your race was a class, and even in first edition AD&D the class determined how you played and how you advanced. You had games where this wasn't the case, and what a lot of systems did as an alternative to the class/level model of advancement was use skills. When 2nd edition AD&D came out it was a lot more skill based and back in the day I thought that this was a good idea. However when playing it it took up a lot of space on the character sheet and it didn't seem to fit well with the class/level system. I thought that the problem was too much class and not enough emphasis on the skills and I gravitated towards games with more robust skill systems. When I made my home brew it was entirely skill based. I could never figure out why the more work I put into the skill system the less fun the game got. I haven't played 3rd or 4th edition but they seem to be a whole nother level of skills and feats and daily and weekly powers so much so that I don't even recognize the system (it might be great fun but it's not good ol' d&d IMHO).
Now I think I had it backwards. I think that bolting all those skills onto a character system rooted in class starts making it harder for players to even try doing things that aren't in their skill list. The mind set isn't there to think outside the box. This makes it harder to play non-optimized characters and it makes it harder for small groups of characters to have the right combination of skills to succeed. This leads to more skill spill over, more multi-classing and special blended classes. I think it can work if a game is built on skills or feats and not class/level progression (e.g. Traveller, Savage Worlds) - but that's not d&d in my mind - it has a different flavour.
Playing Microlite with my family, the rogue player (low on HP from a previous encounter) was asked to check a chest for traps and she refused saying that she didn't want to get hurt. Some bickering occurred but she stood her ground. Finally the fighter player (with lots of HP) said give me that chest. Now the fighter didn't have a good Subterfuge skill but had a decent Mind stat and described how she was looking and what she was looking for so I assigned MIND+Subterfuge as the roll with a DC of 15. She managed to roll well (17 I think) and find the poison needle. What this illustrated to me (and the players) was that the rogue wasn't checking for traps because they were the only ones that could do it - they checked because they were good at it (+3 Subterfuge).
I think this is great and it really encourages players to try things or play characters with a different stat combination that they might normally try. Yay Microlite.
My only problem with Microlite for classes is that they aren't distinct enough after starting bonuses and that some of the benefits or restrictions are based on dogmatic rules rather than mechanics to encourage types of play. For example aside from the sneak attack once per combat ability what encourages players to choose a rogue over a fighter who takes skill points in Subterfuge? Not much.
So now the class bonuses are reinforced as you progress - the non-magic classes get a bump to their skills every 3 levels and the magic classes get one every 5 levels (to be fair since they get the a magic bump too). I tried for simplicity so some more playtesting may show issues with this but it's good enough for now. This is in addition to the chosen skill bump every level so it is still possibly to develop that sneaky fighter character but (s)he'd have to work really hard to keep up with a rogue as they gain levels.
I also used the minSTR and armour mechanics developed by The Wanderer to encourage players to pick weapons that fit their characters rather than simply make blanket statements about usability. Your mage can use a great axe but then she's going to have so many penalties to either magic or strength to make it counter productive. I do cheat a bit on the philosophy by saying that arcane magic is hard to cast when using armour - however it doesn't prevent the player from doing it - it just prevents them from becoming magic tanks in plate mail armour.
As for multi-classing I don't support it. If the only difference in character ability are these mechanical bonuses then you don't need to allow multi classing. You can build a burly mage or a sneaky fighter if you want anyway. Multi classing just breaks things and gets in the way of a good time.