I love d20 Modern, a lot. But even I could come up with a lot of things I'd want to do to improve it (most of which I already use as house-rules):
WP/VP as optional rules.
Subdual Damage as per D&D 3.5 (existing Subdual Damage is incredibly broken/not working!)
Damage Reduction as per D&D 3.5 (additional +'s require to pierce DR is extra-rough in d20M, where magic is ultra-rare, very expensive, and Enhancement bonuses don't go above +3)
Psionics updated to be similar to D&D 3.5
Incantations in the Core rules.
New Craft categories to reflect things like cooking, sewing, and non-adventuring tasks (funny how in D&D Profession and Craft are incredibly open-ended catchalls where you can create new skills to fit your character or campaign., but d20M has a fixed and inflexible skill list)
In fact, get rid of "fixed" Craft/Knowledge skills, keep the normal categories which are used as examples and for official requirements ect (like in D&D), but not explicitly saying you can't create new categories.
Much clearer explanation of the Wealth system, probably the most misinterpreted part of d20M after the Subdual rules.
Some of the elements from Future/Past integrated into the core, like Progress Levels. A little more core support for d20M being used to run games in recent history or near future. WotC treats d20M as the core book for every type of RPG but medieval fantasy, being the de facto Universal d20 System WotC book, so put a little more support for that in the core.
Personally, I'd scale down the details on guns. I know some d20 Modern fans are big gun enthusiasts who want exacting stats for each and every gun. Just like D&D doesn't have separate stats for Claymores, No-Dachis and Zwiehanders, they're all Greatswords, d20 Modern shouldn't have nothing but mostly similar guns (or obscure gear rarely used in the real world, like pull-up armored pouch-vests, as core gear).
Remove most of the D&D monsters from the core, and put in more of the Menace Manual creatures. Grey Aliens, Sasquatch and Men In Black seem much more appropriate "modern" foes than Orcs, Dragons and Ogres. In fact, tone down the "D&D in the Modern Day" motif for d20 Modern, which they were real heavy with early on.