Okay, so here's my explanation of these things. If you still think that it would be better another way after I've explained, then please say so
First off, the table is actually two tables. This was just stupid formatting issues. Sorry. One of the tables relates your result to bonuses, and the other relates your knowledge skill to creature types.
Normally I would group them that way, too. However, I wanted each knowledge skill to have at least one creature type to go along with it. Also, consider the balance issues. With the suggested assignments, who would take the planes over, say, nature? These assignments make perfect sense, and I agree with them, but if they were used for the class then it would discourage the selection of some skills. I would like to have all of the knowledge skills be valid choices.
As for the whole thing about psionics... I'm not sure I understand you. Even though "psionic" isn't a type of creature per se, I thought that it would make sense to go with that knowledge skill. Also, there aren't too many psionic creatures anyways, so it doesn't seem too unbalanced.
About the spells... My idea was to have a class that could function as either a good caster, or a good fighter, but not both. I based both the BAB and the spell progression off of the bard. The Applied Studies class feature is supposed to pull the Scholar up to speed in one of the areas. Also; the area that Applied Studies applies to can only be selected once, at first level. Sorry if the wording was unclear. My hope was for the scholar to be almost as good as other classes in his area (dps, tank, caster) most of the time, then be a bit better than them when fighting creatures of his specialized type.
The fighter bonus feats (or the spells, depending on which you choose) are there so that the class can be a bit more flexible. The idea was that a scholar focusing on spellcasting would use them for spells, while a scholar focusing on mundane fighting would use them for feats.
Thanks for the criticism! If you still think that I need to address one of these issues, then let me know. I'll change things that people think need to be changed, as long as they know why I had them that way in the first place.