LRG won't be releasing "The Simpsons Arcade" or "Turtles in Time" any time soon, either.
Yes, it's all speculation. But it's speculation that is backed up by plenty of logic. When a trademark is featured in a title, it has to be removed from the title before that title can be re-published with different licensing. And licensing can and frequently does change hands. The examples you cited of the Simpsons arcade and Turtles in Time got pulled for very specific reasons. Turtles in Time specifically got pulled because the license holder of the TMNT intellectual property changed hands. Nickelodeon purchased all licensing rights to the TMNT intellectual property and brand. They own all things TMNT now. The game got pulled from digital storefronts because its continued sale would have required a new licensing contract with the new license holder.
But such contracts can be made. That is why the resurrection of older digital titles are possible. It isn't insurmountable, it's just difficult. If LRG got Nickelodeon to say yes, a physical copy of Turtles in Time could happen. This is harder to make happen with major corporations because these deals usually involve very little profit for those corporations. They generally consider such deals to not be worth the trouble. And corporations often make other licensing deals that may currently be in effect, and could potentially block this sort of thing. If Nickelodeon has currently licensed the TMNT brand to a different developer, the specifics of that contract could easily block a re-release of an older digital title. This is the tangled web that you have to navigate when resurrecting older games. Take a look at the legal nightmare that is the "No One Lives Forever" franchise sometime.
And it is actually easy to point the Scott Pilgrim blame on Universal Studios. Scott Pilgrim is not a major multi-media franchise. It only got one comic series, one motion picture, and one video game. No one is currently working on a second Scott Pilgrim video game. No one is licensing the property out to other companies. Nothing is really happening with the property at all. Ubisoft was involved as a publisher, but they don't have any reason to block a physical re-release. And depending on how their contract was set-up, they may not even have the ability to block a re-release. They may have even tried to re-release the game in the past, Ubisoft is no stranger to porting their games to newer hardware. They like making money off of older titles just as much as the next game publisher. One of the other PS3 games that I would love to see hit LRG would be "Beyond Good and Evil," an Ubisoft title.
The original game developer has no reason to block a re-release, the associated pixel artist has no motivation, and the original writer/artist has no reason to block a re-release. It's just a matter of elimination. Universal Studios are the only associated party that has any reason to prevent it from happening. Ergo, they are the most likely target for blame. Their reasons may not be good, but they are still reasons. It may not even be a matter of pettiness. It may just be that they think the profits from the game wouldn't offset the legal cost of writing up the necessary contracts. (which is entirely possible) When you're dealing with a company that large, these things happen.