Before I comment, I would like to tell you where I am coming from. I like the changes to 3.5 for the most part and I feel that it is a marked improvement from 3.0. As to older versions of DnD, I played both 1st and 2nd editions (the latter including the various rules supplements) as well as classic DnD (Basic/Expert/Companion/Masters Sets). At the time I played the older versions, I enjoyed them greatly. But seeing the elegantly streamlined rules in 3.0, I would never go back to these archaic systems.
OK, onto your review:
1. No Playtester Credits
I can assure you that playtesters did, in fact, exist for 3.5. The fact that they chose not to credit them is regrettable, but doesn't affect the quality of the product itself.
2. Unnecessary Rules Changes
Weapon Sizing: I agree with you here, I much preferred the 3.0 system.
Damage Reduction:
I must disagree with you here completely. The 3.0 DR system was flawed on many levels. The first was that the magnitude of DR (typically 20 or more) made attacking the monster with inferior weapons useless. For instance, they may as well have used the 2nd edition convention for Iron Golems (e.g. "requires +3 or better weapon to hit"). The DR values in 3.5 have been reduced significantly. Therefore, if you do not have the appropriate weapon you can still make a difference. Having playtested the new DR extensively, I can assure you that our party has not suffered greatly when fighting creatures with 10/silver or even 15/silver DR even though we did not have silver weapons.
Furthermore, later in the article you bring up the "fantasy mythic" feel that seems to have been lost from 3.5. IMO, the DR system is much more representative of this fantasy feel. If you are fighting lycanthropes for example, you should be penalized if you don't use silver weapons, the classic Achilles' heel of these monsters. Why even bother with silver in 3.0 if you had a simple +1 sword?
Challenge Ratings
These changes were needed to make the game challenging. True 3.0 claimed that PCs were stronger, but ultimately this proved to be too true. Fighting evil Oustiders in 3.0, especially those in the high CR range, was largely a joke due to their inferior hit points and attack bonuses. 3.5 made the CR more in-line with the power of the monster and elevated truly powerful foes such as the Balor and Pit Fiend.
Paladin Mounts
I agree with you somewhat here, but unfortunately it was a necessary change. Equine mounts are simply not suited for dungeon travel and it seems silly for the paladin to leave his horse outside the "ruined temple" every time. Furthermore, the mount is a significant class feature of the paladin and its utility should be a principle concern when trying to balance this class.
Subdual damage: They changed it to nonletha? So what?
Spell Focus: A lot of debate over this one. I'm neutral on the issue.
Power Attack: Before, a raging half-orc Barbarian with a two-handed greataxe had the same power attack/damage ratio as a halfling rogue using two daggers. A welcome change in 3.5.
Major Spell Alterations
I don't agree with all the changes but ultimately it became about balance. Spells like Polymorph, Fly, and Disintegrate simply made the game too easy for arcane spellcasters.
Fantasy Flavor Removal
IMO, this is the core of your argument and it is where, I believe, many of your criticisms originate. I play DnD to have fun, not for a "fantasy" simulation. I want all PCs classes to be balanced with each other. To do this, you may have to make some unwelcome changes. But I, for one, am glad that they did it. I really disagree with you on item creation however. This is one of the great strengths of 3.0 and 3.5. The ability to craft your own items gives PCs tremendous flexibility. Now you can actually spend your gold pieces, unlike 1st and 2nd ed.
Breakdown of "Open Gaming"
Clearly, WotC could have made it easier on the competition, but they didn't. The stronger companies like Green Ronin will adapt, come out with alternate products (like Malhavoc), or go under. I can live with that.