There is a mechanic that mitigates some of the xp that item creation requires that is used by The Artificer (Eberron) and the Fleshwarper (Lords of Madness) prestige class.
I was wondering why the Alchemist doesnt have a similar mechanic? While Mutagens, Extracts and Bombs dont require xp, crafting potions will, which is something that Alchemists are almost certain to do. Im fairly sure that Brew Potion will actually appear in the final class, just going by what ive seen on the forums, so this is something to consider, not just with the alchemist, but with ANY item creation class.
Additionally, i would caution against disallowing extracts to count as spellcasting for the purpose of prestige classes. It would be best to find SOME way to let the alchemist fold into prestige classes, because if you dont, you lose the flexibility that they offer completely.
The Warlock, from 3.5, was extremely difficult to PRC, and so most people just didnt, unless they used the prc's that were put out in complete Mage to alleviate that exact problem. The Binder, Shadowcaster and Truenamer had a handful of mediocre prestige classes published in the book they were, and then never saw support again.
You guys dont put out as many books as fast as WOTC did, which is a strength in most ways; It allows for a higher quality book. However, it also means that you wont be able to offer specialized support for a single class as easily because you need to get the most out of every page you publish. This is another reason i would suggest making the Alchemist's extracts count as spells for prestige classes; You wont be able to easily offer it special support.
There is no mechanic to alleviate XP costs because magic item creation doesn't have XP costs in Pathfinder. Nothing costs you XP to use any more (thank the gods). And at the moment, the alchemist cannot qualify for the brew potions feat anyway (although that will likely be changing, hopefully by giving them Brew Potion for free).