Mewtwo was not just poorly received by people with knowledge of the tiers. Hardly. People didn't like his moveset in general, and it was a complaint among Smashers in general, not just those with competitive knowledge. He wasn't a popular Smash character, people even wanted him cut. That is until he actually was cut. People forget how poorly Mewtwo was received pre-Brawl, and not just from the dedicated Smash community. Why do you think he was prioritized behind clones (but not all clones)? Why do you think he was the only original newcomer to Melee on the chopping block? Sakurai doesn't care for tier placement, but overall character popularity is something he listens to.
Sakurai made cuts last time, but the two-in-one transformation character was spared, even though half of that transformation was largely unimportant at the time of Brawl. If Sakurai cared for ease of implementation above the characters themselves, he wouldn't opt to include programming and gimmick heavy characters like he has before.
I think with the knowledge that Sakurai isn't one to try and save himself effort, he clearly goes above and beyond for his games, unless he is doing a massive trimming of the roster (in which case I still think both Jiggs and Lucario would go before Trainer), he's going to do his utmost to keep the Trainer, a character he's wanted for two games now, and the actual protagonist of Pokemon. Sure, he takes more effort to include, that I'm not debating, but Sakurai has never skimped from effort, and he doesn't seem to be in such a time crunch that he'd change precedent.
Well... in Melee Sakurai confirmed she wasn't one of the latter characters made... because he told us the clones were the latter characters made. In Brawl, from Jigglypuff's lack of SSE role to placement in the data as well as in some roll calls, it's clear she wasn't in the initial wave of characters included. And yes, she's "Smash important", I agree, but that only goes so far. Pokemon Trainer is now "Smash important" (maybe not to the same extent), but he's also main-series important and his Pokemon are just plain series staples at this point. Plus, I still don't see why Sakurai would shift priority around without cause.