I'm basing this draft on a philosophy that many great NFL minds subscribe to. That philosophy is that successful teams need to be built around the three most important positions: QB, blind side OT (usually left OT), and blind side pass rusher (usually RDE, but sometimes OLB). Until those three positions are solidified your team will always be in rebuilding mode.
The 49ers only have one of the three solidified, with Joe Staley at left tackle. So getting a QB and a pass rusher is top priority. I know we need secondary help, but like I said, I just don't think CB or S are as important as OLB or QB.
I'm assuming that there won't be a CBA before the draft, and so I'm leaving free agents and trades out of this.
Round 1 (pick #7) Jake Locker Washington QB
Okay, you can start flaming me now. I don't think Miller or Peterson will be there at 7. But moreover, I really think that with the right coaching Locker could be the best QB in this draft. He has a physical tool set nearly as good as Newton, but has more starts, brains and character. I watched him destroy others teams single handedly his freshman year, and thought to myself, "if Alex Smith doesn't work out I want this guy to be our next QB." Then last year when it seemed like Smith was not working out I thought, "damn, too bad we won't be drafting high enough to get Locker." But he stayed in school, hurt his draft stock and now could be right there for us. I know people will say 7 is too high, and that we could trade back and still get him. Sounds great, but I don't think he will last many picks more. With Washington, Minnesota, Tennessee, and Miami all picking after us, I think there's a good chance he's gone by the mid first. And I'm not sure who we would trade back with that wouldn't use our pick on him. Like I said, QB is the most important position in the game, and we should be trying to get the best prospect we can possibly land, not trying to get a good bargain.
I also like Ponder and Kaepernick, but I'm not sure I'd take either at 7.
I also like Ponder and Kaepernick, but I'm not sure I'd take either at 7.
Round 2 (pick #45) Justin Houston Georgia OLB
I think with all the QBs that will get picked early, and all the D line talent, Houston could still be around at 45. And Houston looks like a beast at OLB with great speed and athleticism for a guy his size.
I also like Acho and Moch here if Houston is gone.
I also like Acho and Moch here if Houston is gone.
Round 3 (pick #76) Ras-I Dowling Virginia CB
Maybe not as good as the elite CBs, but still seems like an experienced college player with a good skills and a great head on his shoulders.
If he's gone I'd take Johnny Patrick instead.
If he's gone I'd take Johnny Patrick instead.
Round 4 (pick #108) Shane Vereen Cal RB
I loved watching this guy at Cal and I think he's exactly what we need on the 9ers. He's fast and shifty enough to be our change of pace back and work as a return guy. But he's also big and strong enough (31 bench reps!) to be an every down back sometime in the future. Also great catching the ball out of the back field.
Round 4 (pick #115) Sione Fua Stanford DT
I think Franklin will end up signing a long term deal. But we should still look for another NT and Fangio knows Fua well.
Round 5 (pick #141) Greg Salas Hawaii WR
Has the toughness to go over the middle as a slot guy, but enough talent and size to possibly be a starter some day. Would be a nice complement to Crabtree and Morgan.
I would also be very happy with Jeff Maehl here.
Round 6 (pick #174) Ahmad Black Florida S
I actually think safety is almost as big a need for us CB. But I would like give Mays a chance to develop. Still, if we could get a safety with Black's passion and skill this late it'd be a big win. I think he might drop because of his small size, but could still be a great nickle player and special teamer despite that. Think Bob Sanders.
Round 6 (pick #190) Casey Mathews Oregon LB
Okay, this pick is mostly about genetics. But even if he doesn't turn out to be as good as his brother, he could still be a great backup ILB.
Round 7 (pick #210) Owen Marecic Stanford FB
I've seen this guy going much higher on some mocks, but I really don't think anyone is taking a FB high unless they put up Jacob Hester numbers. Still, I think Marecic could be a solid FB for us, and put his LB skills to use on special teams.
Round 7 (pick #230) Adam Froman Louisville QB
We need more than one QB and this local kid has real physical tools. He's similar to Locker in many ways, which I think would make him a great back up if he can develop. Plus, I gotta go with a fellow SRJC alum. 
Devlin is another QB I'd love to get late.
Devlin is another QB I'd love to get late.
Round 7 (pick #238) John Clay Wisconsin RB
Figuring he'll probably end up on the practice squad. But it's always good to have extra RBs available. And while Clay isn't the greatest (or fastest) all round back, he's a monster on the goal line (41 career TDs!).
Round 7 (pick #249) Jarriel King South Carolina OT
We'll probably want another O lineman. Sounds like this guy has some talent, but should be there late.
I think this mock covers most of our pressing needs and nets us many of my favorite players. Top to bottom, there's a lot of guys I'd love to see on the niners.
Flame away.
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