So, supposing I have a level 3 Alchemist with an 18 intelligence. My bombs would do 2d6+4 damage, and on a crit, I would do 3d6+8?
How well can an alchemist stand in for a rogue? The only thing the class seems to lack is a way of dealing with magical traps, and is that really a big deal?
Secondly, I am not very clear on how their extracts work. Is there a chance for spell failure when using them? Is the whole "potion" treated like a spell component, and you just drink it, or is it a little more involved than that? Do you have to decide in advance what spell it is, or do you decide that at the moment of "casting"?
What do alchemists typically do when they aren't flinging bombs? That is, as a class, by themselves.
What other uses are there for the "Throw Anything" feat? What if I threw a chair at someone? Or a tindertwig? Or a halfling?
I think it is important to realize that these classes do not exist in a vacuum.
Yes, a wizard has decent skill points thanks to his high Int (but not from his class) but wizards have much more appealing skills to spend their points in than stealth. If a wizard wants to be stealthy, he memorizes spells. He doesn't spend ranks in stealth, unless he is multiclassed with a stealthier class.
Yes, a wizard can cast invisibility, but he isn't silent. An invisible wizard sneaking past guards is undoubtedly sweating bullets. They may not *see* him, but that doesn't mean he goes unnoticed. Stealth is more effective in this regard, being able to prevent others from noticing you at all.
Climbing? Spider climb is nice, but duration is a problem. If you climb a wall, chances are you are going to have to climb it again later when you make your exit. The same with fly. You can fly to your goal, but how will you get back?
Yes, a wizard can do these things, but they cost resources. Resources that a wizard would probably rather spend on things that they can do well. In short, rogues are free. Wizards have their hands full.
Rogues aren't as tough as other fighters, but their defenses are nothing to turn your nose up at. Dex and light armor is just as valid a means of getting to a high AC as heavy armor and a stout shield. Plus, they have a reflex save to die for, and evasion to go along with it. When the rest of the party is biting their knuckles from the pain of that last enemy fireball, the rogue just shrugs, brushes the ash from his shoulders, and gets back to stabbing the wizard in the back with pointy objects.
And if things do get dicey for the rogue (and things get dicey for any character no matter what hat they wear) they have the most ability to get back out of it. In my experience, when a wizard is in trouble, it's because he lacks whatever spell it is that he would ordinarily need for the situation. (whoops. I guess I should have prepared feather fall today. Darn.) Whereas rogues have all the versatility they need to escape that pickle they have gotten themselves into. A wizard caught in the grasp of some tentacled beast is probably moments from death. Rogues take escape artist just for this reason. Don't think of this as a quality to make up for how "bad" the class is. This is an extra layer of defense that the rogue has that many other classes do not. If there is a skill that will get them out of trouble, and save their bacon (or the party's!) chances are good that the rogue has it.
Personally, I don't even know why this discussion is even necessary. Sure, rogues have their problem moments, and usually it involves foes that cannot be sneak attacked. But I don't think I have ever sat down to a game and thought to myself that rogues were sub-par as a class. They are one of the classic four roles of an adventuring party, and they fill out their role well. I think that speaks well enough on its own.
Here's my 2 cents...
According to the actual page for the trip maneuver, it is never described -what- your character uses to make the trip attempt, provided it is a melee attack. It could be your foot, a stick, a banana, or some exotic weapon you picked up off the ground.
Weapon bonuses do not figure into trip attempts. Whether I "use" a +5 holy avenger or a stick of butter to make a trip attempt, the cmb is still BAB + Str Modifier + Special Size Modifier.
Weapon proficiency doesn't figure into trip attempts either. The only thing that matters to figuring attacks of opportunity is whether or not you have the improved trip feat. This is also thanks to the trip maneuver's vagueness. At no point does it ask if you are proficient in the weapon you are using (because, again, it never specifies if you are using one or not!)
Trip weapons are special in that they are the only weapons that specify that they can be used for trip attacks, and offer bonuses for doing so. There is nothing stopping you from using other weapons, but it hardly matters-you get nothing and suffer nothing from doing so.
Edit: had to make a couple changes. There are benefits to tripping with non tripping weapons, like a Glaive or a Lance. Reach. These weapons are still melee weapons, so can be used to trip.
So ultimately what makes a weapon a good tripping weapon is it's reach, not necessarily whether or not it has the trip ability, though that may help against high CMD opponents.
But that's just my opinion, so ignore it if you like.