Couple things. I hate the way Wade gets that extra free throw. And it's not just that one extra free throw, it's a lot of the free throws he gets. He's always been that player trying to run into defenders in order to get refs to bail him out and put him on the line. I'm not saying Kobe never tries to get to the line, but he takes fewer shots than Wade where he has no intention of actually making a shot but of only getting to the FT line. I'm not arguing about effectiveness in that aspect, cause getting to the FT line is obviously the most effective thing you can do in basketball, but it's not how the game should be played to me.
That said, in terms of stats- Wade doesn't shoot 3's. Career 3-point % of less than 30 (which is putrid for a two guard in this day of basketball), and he takes less than half as many as Kobe does. So of course that's going to help his overall shooting %. Kobe's 3P% isn't spectacular at 33-34, but it's respectable enough. That's a part of the reason for the FG% disparity. Wade shoots a few% higher on 2's, Kobe shoots about 5% higher on 3's, which is about a wash to me. Kobe also shoots FT's significantly better over his career than Wade does. 7% is a big difference on FT's. Personally, I'll take the guy who has a better chance to stick a 3 or hit that free throw when he does make it to the line because of how big both are at the end of games. On the flipside, refs should not be as willing to bail Wade out at the end of games for creating contact so his higher FT attempts won't translate as well in crunch time as the higher 3P / FT % of Kobe will.
And yes, when comparing careers Kobe's longevity vs. Wade's can't be overstated. Including playoffs, one guy has played 53000 minutes and the other has played 30000. Wade will bridge the gap some because he should play a few more seasons after Kobe retires, but it probably won't be all that much considering his playstyle and all his physical issues.