I'd probably just do a Poisoner (Rogue) with the Master Alchemist Feat.
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Well
1) you could try to take an archetype that removes the bomb class feature like vivisectionist and replaces mutagen with the thing that increases mental stats (I forget how to spell it)
2) play a wizard or something else int based that has a flavor text relating to more scholarly exploits because
3) see if your dm will let you use some of these http://www.realmshelps.net/magic/items/alchemy.shtml
http://www.realmshelps.net/magic/items/alchemycharms.shtml
http://www.realmshelps.net/magic/items/magicplants.shtml
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Next there's flavor/background/RP stuff
You could play a sort of bookish fellow who wants to record and document the various magical and alchemical uses of flora, fauna and mineral and discover and document entirely new wonders
A member of the local assasian's guild who wants a leg up on his competition and wants to use various alchemical reagents to strengthen himself and his poisons
An entrepreneurial cad who wants to find these valuable plants and other reagents and plant them to farm and sell them at a massive upcharge
My first thought was to sarcastically say Investigator, because it's technically not an alchemist. But, to actually answer your question, you could play a half-elf alchemist with the Bramble Brewer racial archetype. Although it is an alchemist, it is very wilderness-themed, so I feel like it would work.
As for fluff, you can say that this alchemist is searching for rare and exotic ingredients from the wilderness, so they they can experiment with nature.
Check the Alchemist archetypes. Some new ones ditch both bombs and mutagen.
Investigator is your best bet, though! All the alchemy, none of the explosion. You'll be great at skills, and at fourth start picking up some combat abilities.
The alchemical items introduced in the alchemy manual have recipes for their creation listed. If your GM is willing to work with you then you might be able to find the required reagents or suitable substitutes out in the wilderness. If they're not forget that idea, by RAW you can only buy the reagents. There are some feats to improve your ability at making those items.
I have actually two Druids in two different campaigns with Craft: Alchemy and I love playing them both, one a dwarf (earth domain) the other a ratfolk Urban Druid. Lotsa fun.
Just throwing out some ideas here. I'm about to start a new home-brewed campaign that deals with a lot of wilderness exploration. I had the idea of an alchemist who is always looking for exotic ingredients. But a bomb-chucking, Mr. Hyde-type mad scientist concept doesn't really fit my campaign feel, so I'd rather not use the alchemist class.
The alchemist class isn't locked into that mode of play, especially with archetypes.
Actually an Investigator may be what you are looking for. An Empiricist is about as far from a mad scientist as you can get.
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Vivisectionist Alchemist
Inspired Blade Swash 1/ Viv Alchemist
Investigator
Inspired Blade Swash 1/Empiricist Investigator X (AkA Swashigator)
Both very skill-y and very rogue like. None Have bombs but you still get extracts to chug which you can flavor up if you like. You can easily Build them not to become some crazy Hyde beast but more a refined science with the grace of a Rapier (or other weapon). They won't be the strongest combat style character but will be effective in most situations with the utility, skills, and half decent combat abilities. I would say the Str Based builds are more combat capable while the dex builds tend to be better in the skills department.
You could run with a Witch and pick up Cauldron Hex. You could also run something like a Hunter and make alchemical arrows in addition to whatever else. Alchemy in itself is one of those skills you can plug into just about any class for an interesting bit of flavor.