I really couldn't tell you if it's better or worse. The 3.5 PHB seems similar to the 3.0 PHB in its general organization. If you knew where it was before you'll be able to find it now.
The 3.5 MM has a lot of its rules stuff in the back (the book is divided in to chapters, now -- ch 1 is the alphabetical monster entries, ch 2 is animals, ch 3 is vermin, ch 4 is advancing monsters, ch 5 is making monsters, ch 6 is monster skills and feats, and ch. 7 is a big glossary for all of the monster info (different types and subtypes, special abilities, etc.).
The 3.5 DMG has been rearranged the most in my opinion. It's going to take some getting used to.
Ch 1 -- Running the Game
Ch 2 -- Using the Rules (things like movement, bonus types, combat, saving throws, and the XP system)
Ch 3 -- Adventures (types, encounter level, treasure tables including gems and art, dungeon terrain/features, traps, random encounters, wilderness adventures, urban adventures)
Ch 4 -- NPCs (NPC classes, stats)
Ch 5 -- Campaigns (world building, adventuring on other planes)
Ch 6 -- Characters (Ability scores, races and subraces, monsters as races, classes, prestige classes, special cohorts, familiars, mounts, animal companions, epic characters)
Ch 7 -- Magic Items, creating items, special materials
Ch 8 -- Glossary: divided into three glossaries actually -- Special abilities, Condition Summary, The Environment
Visual Aids
Index
I haven't read enough to say whether there is adequate cross-referencing between sections or between books, however.