I like the concept of Personal Alchemical Reagents as a resource they use for the creation of their items. Separating them from resonance seems like a great direction.
I like the expansion of Alchemical bombs having multiple levels now, as it opens up non-alchemists up with the ability to use some of these items at higher levels if they so choose to and have the money to be able to afford them.
I honestly thing this is a really big bonus to the game as a whole, provided by some reworking of how the Alchemist will work.
However, I think that alchemists, or at least Bombers should get to a bonus die of damage (or for instance points of various splash|persistent damage) when they personally throw/set off the bombs in question.
I also think these items (if created by the alchemist or bought/acquired otherwise) when used by the alchemist should have the DC associated with the save boosted to the alchemist's class DC if it is higher, and not solely based only on the item DC. I think this should be able to apply to to Chirurgeon's elixirs and poisoner's poisons and such. Actually, I'd be fine with the DC effect being applicable for all alchemical creations used by the alchemist in question, not just the ones they specialize in. But potentially poisoners might get extra die of damage from poison, and Chirurgeon getting an extra die of healing as well potentially.
Also, I'm reminded of something that bothered me from the beginning. Quick Alchemy. Allow it to make items that are good until the end of the alchemist's 'Next' turn, not just usable during same turn in which they were made.
Advance alchemy, in my opinion, they shouldn't have to be all created at the start of the day, although I'd be fine with any made later in the day requiring a 10 minute stretch of time to make each batch. It seems implied you might only be able to make the 24 hour versions during your morning preparation time.
Someone else mentioned, that while Mutagen alchemist start with the ability at 1st level, I think the other alchemist should gain access to those types of alchemical items naturally at some point further along as they level up, like they used to. I agree that they should get that access.