I don't want to be abrasive, but I'm going to argue a little bit about some of these changes, because in looking through Kholai and Eldest's various discussions, I get the idea that both of you are approaching this from such an extreme powergamer angle that it becomes completely irrelevant to discuss. While optimization is part of D&D, at the highest levels it simply becomes asinine. Especially considering that Kholai's proposed Engineer hugely complicates the Engineer in order to get around a fairly minor balance issue. Alright, maybe not fairly minor, but still, I think reducing complication is one of the reasons people play E6 in the first place. The proposed change to Engineer creates a weirdly fused skill and point based system that, while balanced, would be hell to figure out for an unskilled player. I see no reason why E6 should be an advanced way to play Dungeons and Dragons, rather than a simplified way.
Also, as a DM, if my players tried to pull half of the crap you described in reasoning why the Engineer is more powerful, I would shut them down faster than you can say "overpowered". I think that, instead of tweaking each and every class so that they cannot be more powerful than others, you leave those extremely unlikely and rare cases where someone breaks the game in the hands of the individuals who run games using these classes. Some tweaking is necessary, but D&D isn't played in a vacuum. There are people on both ends, and if some DM allows one player to abuse the system, he isn't a good one.
I'm running an E6 game right now using this system, with some relatively new players. I have trouble getting them to use Vancian magic, as they'd rather just use the simpler attack system. I don't want them being discouraged from the Engineer class because it got "balanced", into a system that takes knowing the entire system of crafting, and several other books worth of alchemical items to effectively use.