I'm pretty sure Dedede mains have more to complain about with their gordos. I don't think it's something that Bowser Jr. really needs, when he could be buffed in several other ways. Like usual, you can't wait for a buff and have to work around it.
All item moves in the game are balanced in some way because they're also OP just for being items. The same trait that all of them share is that they can all get picked up; but this brings up something.
Even if someone picks up the Mechakoopa and throws it at you, you can also catch it out of the air and throw it back. Also, if they keep trying to pick it up, then punish them before they get it (like what Dessa just said), because at that point in time their actions will be completely predictable, and you don't get that a lot in a match.
Other than that, just try to make sure the opponent doesn't get the Mechakoopa. Launch it in the air when the opponent can't interrupt it so that you can get it during the bounce. I'm not an expert on BJ or anything so just watch pro matches I guess