Power Creep and Inflation have to be understood before they can be solved as problems. If you look back, D&D 1e originally started with powerful magic and weak physical attacks—spells had no or few damage caps and a properly worded Wish could do ANYTHING, while characters making melee attacks were limited to, at best, 2 per round with even a high level fighter inflicting somewhere around 2d6+10 damage per attack. Since those days, magic has gotten progressively weaker and less useful while now characters can easily make 5 or 6 attacks per round and are capable of inflicting hundreds of points of damage in a single round!
Regarding the original points of the OP:
An extra +2 to any stat doesn't necessarily increase the power level of the game, but of the PCs. This gives them an extra +1 on attacks, skills, damage and saves and with the glut of available modifiers a +1 bonus just doesn't make a big enough impact. It certainly won't matter for that 10th level Fighter with a +25 BAB who is going to hit just about any enemy so long as he doesn't roll a 1. The 1 point of extra damage isn't going to matter when a character has 1 extra hit point per hit die. Is it inflation? Absolutely. Necessary? Not at all. Especially when the DM is likely going to give monsters more AC, HP, etc., to make their monsters more challenging to the players. Power difference stays roughly the same while only the numbers increase.
Easiest solution is to drop/ignore this bonus or have it only apply to scores less than 10, that way it can mitigate negative modifiers without increasing positives—this not only solves the point of inflation, but power creep as well. And another solution is to provide a +1 bonus at every 4 points instead of 2. Instead of +1 at 12 and +2 at 14, give a +1 at 14 and a +2 at 18. This has the benefit of making the +2 extra bonus important without it really increasing the overall power while also reducing power creep and negating the problems of inflated stats.
Feats every even level:
This is easy. Just require that every 4th level, the character must spend their feat on something related to their race or class. Have rogues spend it on a skill based feat while wizards buy a magic related feat (Item Creation, etc.), while Clerics can spend on Divine feats, and Fighters can spend on feats that don't make them necessarily more powerful, but more versatile.
Class Redesigns:
Simply incorporate prestige class abilities as accessible class based powers. For example, allow a Rogue to take Death Attack as one of his Special Abilities at 10th, 13th, etc., and do something similar for each class. This eliminates the need to have to take a prestige class especially when players only want one or two abilities from a 10 level class. You can also incorporate other class abilities too. If a Fighter wants to be able to Sneak Attack, instead of multi-classing as a Rogue, he could get Sneak Attack as a combat feat maybe once every 5 levels or so, or a wizard wanting a combat feat could get a Fighter's Bonus Feat instead of a spell based feat at 4th level, rather than having to multi-class. Even allow duplication, to a degree. If a 4th level Paladin wants to Smite Evil more than 1/day, he could use his feat to gain an extra 2 uses per day, whatever.
Standardize HP to BAB:
The OP complained only that the numbers were too high, but they are fine at D6 HD = ½ BAB, D8 HD = ¾ BAB, d10 HD = 1 BAB.
But here is where the crux of the power creep/inflation issue lies. With the advent of 3.0, D&D dramatically increased the ability to inflict damage without providing a proportionate means of negating or ablating damage. HD are basically the same, but damage output is through the roof! The easiest way to solve this entire issue is an extension of the above: Standardize damage to HD and BAB!
If you have D6 HD, you have ½ BAB and can inflict a maximum of 1d6 damage (per target) per round; D8 HD get ¾ BAB and inflict 1d8 damage, while D10 HD have 1 BAB and inflict 1d10 damage per round.
Of course there are exceptions such as with magic, weapon specialization and such. But the point is, bring damage output back under control and all of a sudden, gobs of hit points become unnecessary. If a wizard starting with 8 hit points is faced with a goblin, he not going to be AS scared when he knows the goblin can only 1d4 or 1d6 with its attack. He knows he can take at least 1 good hit and maybe 2-3 before he is in trouble.
I would count the + bonus of a weapon as an exception to this limitation. Now, most players I know tend to get +1 weapons and just load up with enchantments (Keen, etc.). But with these rules, a +3 weapon becomes pretty powerful once again.
Spells would be another. Once again, that 5th level wizard's Fireball suddenly seems more terrifying when it can “break the rules” and deal 5d6 damage instead of the 1d6 a wizard can normally do. What fighter or rogue now is even worried about a 5th level fireball? A fighter or cleric has a 50/50 shot of making his save and having enough HP to soak it up anyway while a rogue is most likely going to evade it, only another wizard is going to be worried about a 5d fireball!
Starting HP:
Just give the PCs a bonus/fixed amount. They get their max HD at 1st level, roll the rest. In addition, they all get an extra 6hp at 1st, 4hp at 2nd and 2hp at 3rd. This gives that extra 'padding' that helps keep them alive at the lower levels without making them exceptionally tougher at mid and high levels. You don't need to house rule anything, adjust or create new feats, just give them this bonus and they should have plenty of HP to get through encounters without having to worry about getting killed in a single hit.
Favored Class Bonuses:
I say scrap the whole Favored Class concept anyway. Its pretty damn weak and doesn't provide any real benefit. Its nothing more than a nod to older editions of D&D for those who think most dwarves should be fighters and most elves, wizards. If any race can be any class, this concept needs to go completely out the door! Give a dwarf more hit points because he wants to be a fighter instead of a rogue or wizard? How? Where exactly does it come from? Why should a dwarf fighter automatically have more hp than a human or halfling fighter? Where is an elf wizard getting his extra hit point in comparison to the half-orc wizard who took the same classes, studied the same magic?
