Logistically this was a sound move. Though he had a small sample size, he was developed by the patriots and got to observe and learn from one of the best QBs in the game ever during that time. Plus Shanahan wanted him as much as he did with Cousins coming out of college and has observed him for a long time. The niners like the Browns did make a play for him, but the Pats were not interested and the niners were not going to give u the farm. The Patriots did not want to move him in the off season, because they were unsure about Brady going past this season. Now they feel Brady (along with Brady himself), in addition to this season can also play another 2-3 more seasons. During which they felt, they can probably and develop his replacement then. So rather getting just nothing for him, they moved him now. The pats never pay players more than they have to-look at some of the players that have left. So they were not going to pay someone who was going to sit and Jimmy was not going to wait.
The reason the niners acted now is that they want to get it out of the way as far as the possible future franchise QB was concerned. Rather than react and wait for the market, they took charge. Cousins, as dumb as it might sound, might yet again get tagged. Then all the other teams who would opt for trying to get Jimmy would go for him also and there would be no guarantee the niners would get him. This way the niners can start getting him familiar with the offense already plus the off season rather than just an off season. Ryan took a whole year and he had a more talented group. Also remember the niners can tag him and depending how they tag him either just match any offer which they would have no problem with or let him walk in which case the niners would get two first round picks making it like the niners traded the high second pick for two first rounder. The niners could then use their first on a franchise QB if they wanted and draft two other highly touted possible starters.. However, I think the niners are more likely to sign him. Either way a win.
Also, although his sample size is small compared to Cousins, Jimmy is much younger. Mike has followed and scouted both and like I mentioned earlier Jimmy tutored under the best.
Now also, the niners can also, trade their 1rst round pick for a kings ransom especially if the QBs come on strong.and one team, which is all they need, gets enamored with a player. Shore up the talent and depending how they draft hit FA if there is a player(s) that are worthy.