I used to run Modern a lot, but I now believe the best game for modern or sci-fi is something rules-light like Fate.
I really liked talents, but gradually realized I was the only one who did. Every single third-party product seemed to hate them, and found themselves crammed with Advanced Classes, many of which really should have been Prestige Classes. I recall a line of adventures where they introduced Advanced Classes you could take after only two levels, which meant that if you allowed those rules nobody would ever see two talents. (Unless they took a chain of broken feats from d20 Future.) I can say lots of good things about d20 Modern but virtually nothing good about d20 Future.
When I ran it I found a few house rules were necessary:
Many mental talents needed more explanation. Plan and Intuition, for instance. Players ignored some great clearly-explained talents (eg Faith).
The Fast class Defense bonus went from +2 to +8 (instead of +3 to +8) to avoid snatching up one level of it. This also meant the combo of BAB and Defense for Strong and Fast matched each other at every level. A Fast 1 had BAB +0 and Defense +2; a Strong 1 had BAB +1 and Defense +1; both match at +2.
You need fractional BAB to avoid nerfing multiclassing too much.
The Profession skill is messed up, since spending Wealth is largely unnecessary beyond character generation, except for a few types of PCs (eg crafters). There were no maintenance costs (eg rent), and it damaged motivation to "adventure". I found the best thing was to strand the PCs in the middle of nowhere so they couldn't just get back to their day jobs. Honestly stealing Alternity's resources system would work better.
A few rules were needed to make guns gradually better over levels. For instance, I thought of making Dead Aim a standard action but give a damage bonus in addition to the stated bonus. I created a few feats to bump shotgun damage at short range and was working on something for pistols too.
Grenades didn't work too well, being too "contained". I think the best nerf was, ironically, to make them splash over a wider area. Given the close quarters PCs often fought in, nobody would want to use grenades.
There were balance problems that I couldn't figure out. Bodyguards could take damage (Harm's Way is a great ability) but couldn't dish them out. There were basically meat walls that added extra hit points to their principal. Why be a Smart/Techie when the Smart Hero's Savant ability is just so good?
