So after thoroughly reading through the class, I can say I love the idea of the alchemist and I'll be playing one starting this week. However, the more I read the class the more I see some glaring problems which I have to say is discouraging.
1. The discoveries well....they would be amazing if you got enough of them as it is now there are 24 discoveries (not including grand discoveries) and I get to pick 6? Only 4 before 20th level and to be honest you're really limited by the pre-reqs. I would say making it bombs every odd level and discoveries every third level starting at 1st would make them a lot better.
2. Bombs are well once again they would be good except its a full round, move to mix standard to throw... to begin with it's worse than swinging a short sword, and as things progress it really just doesn't catch up in power level even with its great damage progression. If you could prepare them as a swift action then sure they would be useful or if you could prepare them at the beginning of the day and then have them ready for use all day that would help too.
3. Extracts seem to me like they could be better, and I mean that I don't like taking a round or two so I can be useful, that seems unnecessarily limiting to the alchemist. Why not instead make it quicker to quaff a potion then I buff the first round then get to participate in the battle starting in round 2 much like other spellcasters who buff the first round then start to do things.
4. Mutagens I really can't complain about these they have good flavor and let you become a combat monster for a fight which is interesting, I really like the flavor of a self serving caster hybrid.
Ultimately, I think you could fix this class just by making swift alchemy apply to the creation of bombs (so they become a swift action), make discoveries a 1,4,7....progression adding more poisons and alchemical items and make alchemist be able to quaff a potion as a move action or a swift (wishful thinking). I'll try the class as it is for now and then try it with these fixes and I'll be sure to let everyone know pros and cons.