I'm pretty sure (hoping) Discord's playing the long game now, which might be the only thing that would redeem the current writers for season 3 and EG. Heck, for all we know he wasn't even really trapped as a statue for all that time. He could have simply time traveled into the future (time travel is canon, even for non-deity like beings -_-) to a point when he thought the vines would have taken over and got rid of the EoH already but, he just arrived early by a few years and decided to mess around for a bit. Now that the EoH are tucked away in a tree, all he has to do is wait for one of the bearers to die or just move the entire tree somewhere else (I'd go with the Moon, seeing as the EoH seem to be required to get there) so that the ponies can't find it.
The time travel spell were for like ten seconds back in time, and i don't think Discord even knew about that spell. If he did, then Equestria would have already been his. (I understand that something like that doesn't sounds like him, but lets face it, Discords episode came before the time travel episode.) And he WAS trapped as a statue for all that time, i guess he just didn't think so much about the seeds when nothing happened when he came out. It's like a joke that no one understands until many weeks or months later (in Discords case, thousands of years), it's just not funny anymore. And now that the tree of harmony has it's elements back, then i don't think Discord can even touch it. AND, if one of the main six died, remember that Celestia and Luna can still use the elements.
You know how fanfiction is there for people to express ideas that aren't likely/ever going to be put in the show? This is an example of you reacting seriously to a paragraphs worth of fanfiction. Good job.