Between rally and advisement, these attack bonuses are going to get pretty damn big, man. It also seems like you get enough uses of rally that you can use it in every fight. This kind of drinks the Bard's milkshake.
I am also somewhat adverse to a class based around favored terrain as it forces a GM to feel like a jerk for wanting to take the adventure to strange new lands.
I actually sort of like these roll-heavy abilities but maybe they could be simplified. There is just waaaaaay too much book-keeping here. Every other ability has a resource pool that must be kept track of separately. Adaptive defense is sort of goofy. It is like a worse version of snake style.
I also think Secret Wizard is incorrect in saying this class has too many options and rolls (see: spellcasters).
I do sort of like the idea of a class built around skill use in combat.
That would be a Lore Warden. The Lore Warden's Know Thy Enemy feature is very very similar to the Expeditioner Fortes based on Sense Motive.
I think that's a point in favor of the Lore Warden as varied Knowledge skills for each enemy makes it more flavorful than simply being really good at universal psychology.
The name is a little strange. Reading your opening description, I think the name Explorer would be a better fit. On the one hand it seems to be a wilderness class, on the other a treasure hunter, possibly? I'm having trouble getting a good read on your vision for the class. Maybe a little more detail here.
The skill list looks a little funny, but I can't put my finger on what it is. Is it meant to be like the bard list?
Why did you choose to grant proficiency in all martial weapons? I can't think of another 3/4 BAB class that does. taking a cue from the rogue or bard, you could grant simple weapons and also a short list of extras.
Advisement is a fairly weak ability with a long write-up, with the exception of the attack bonuses. If I were writing this, I would shorten this up and provide more general benefits. Bonuses to environmental hazards and disease are pretty narrow in focus.
Traveller's Lore is fine in concept, but the list of skills is too long and scattered IMO, and I would follow the convention of adding half level to skills.
Allowing the choice of any bonus feat doesn't sit right with me. Every class that gets bonus feats has a restriction on what can picked. Fighter has combat feats, ranger has combat style, rogue talents grant access to only a few different feats. I would prepare a list of feats that you think are thematically appropriate or define what kind of feats can be picked.
I like Improved Saves, but would be inclined to simplify it to a d6, regardless of level.
Thanks for the responses everyone, I have been racking my brain all day trying to find a way to make this class a bit more organized and a bit more thematic.
I know 100 percent that this will be a scout class and it will be all mundane, but I wanted it to be more that just a 3/4 bab ranger or a slightly better version of the rogue.
I agree that the name expeditioner doesn't exactly fit the bill, and I am probably going to change the name somewhere down the road. Wayfarer is probably the best alternative I can think of.
An idea I have been kicking around is creating a series of Paths (something structured similar to an oracle mystery) that would have a group of fortes that you could choose from instead of having to pick from a huge list. This would get rid of the Skill ranks as prerequisites completely, and allow me to replace the bonus feats with path feats (feats that you choose from a small pool of options).
However I do feel like outside of the forte's and skill boosts, I need a mechanic that will help it make it's own attacks in combat, something kinda like inspire courage but with a bit more flavor and crunch to it.
Here is an example of the direction I was thinking about going, I would make each expeditioner pick a path at level one and go from there:
Path of the Physical Paragon
Associated Skills: Climb, Sense Motive, Swim
Path Focus: An expeditioner uses his class level as his monk level for determining the damage of his unarmed strikes. An expeditioner who selects this path is always considered armed even when not wielding a weapon.
Path Feats: Improved Unarmed Strike, Great Fortitude, Combat Reflexes, Power Attack (would build on this)
(I would build on this list too)