Personally... I have mixed feelings about LaBeouf in general. I know that in Transformers it was largely a fault of the idiots who wrote the thing, but it was also not a role that the guy really felt right in. I also don't care much for the guy as a person from what I've seen of other things he's said and done off screen.
I also don't know why people keep shoveling blame onto Megan Fox, because from what I saw, she was by far not the reason Transformers 2 sucked. In fact, I thought they just stuck her in a few scenes to say "look, it's Megan Fox, like our movie" or something. I like her, but I can't say for better or for worse what I think of her in general.
On the topic of Indy 4? I actually didn't even realize it was him who played in it until I'd seen Transformers. I don't think it was really all his fault that the movie wasn't as good as it coulda been. I still liked it a lot. I blame Lucas, because the guy clearly can't make movies anymore. The New Trilogy shoulda been proof of that.