Most of the issues IMO are not with that. Most of the "I don't like 4e" comes from:
- Actions specific to WotC: canceling the print Dragon/Dungeon, the way 4e was previewed/comments by the designers, lack of OGL. The layout of the books (limited fluff, uninteresting reads; the PHB and MM are all numbers no fluff). There were people outraged that the gnome/half-orc were not in PHB1 and Frost Giants weren't in the MM1.
- Less simulationism, more gamist nature of the system (see the nod to Realism threads).
- The way the system "Feels" (i.e. videogamey): marking techniques, fighters with "p0werz", the way healing powers work, the "sameness" of classes, etc.
- Lack of some traditional D&D rules: vancian magic, shift from daily resources to encounter resources, over-emphasis on grid-based minis, lack of non-combat abilities (the Crafting Skill, charm person).
While they were working on 4e, they used certain design elements in late 3e books. Complete Mage had feats that allowed an at-will-ike spell ability, there was the Warlock Class who only had At Will powers, the Book of Nine Swords were a 3.5 interpretation of fighter/warlord powers. People complained about those for the video-gamey/non-realistic elements then. Many of the arguments today are the same arguments had when 4e was being previewed.
The above elements would have have existed regardless of the DMG's advice. Once an impression was made about 4e, what the DMG
actually said would not matter. And in my experience, people who passionately do not like something will find more things to dislike about the thing they dislike, and positive elements/counterpoints will have
no impact. There's more psychology behind it but I think that's enough.
Most of your "I'm having trouble running 4e" issues come from running skill challenges (which more has been written than any other topic), building encounters, and issues with the system itself (the bad math and feat taxes, etc). Nothing the DMG would resolve.