Even though we are limited by the animations we have captured, the scenario you describe above should never happen. Can you give more details...
Were you on defense? Which throwing interface were you using? Did you use the maximum throw effort if your throwing interface allows for input? Did you preload the throw before the ball was attached to you fielder's glove?
Please attach a video. There are instances in which an infielder will "take his time", but it should be in an appropriate situation and he should still get the out.
I have yet to see a video of the scenario you described above, and finally seeing one could go a long way to resolving any bugs. In many cases in which I have spoken to someone having a similar issue, I have been able to point out certain "user error" problems that resolved the issue for them. Or...there may be some hole in our throw animation set, but we have worked hard to fill all of these gaps.
Whatever the case, a video would help.
As far as the base running, I know at some point there was logic/code written that would slow the runner down on "sure" outs. I'm not sure if that feature made it through during the rewrite of the base running code this past year, but if not, I will point it out to the appropriate parties.