I really enjoyed the character of Walter, he can heal and regenerate tissue. This was a big part of the Walter viral marketing, the fact that he has this upgrade. He even used it when stabbed in the neck, it took him a few minutes to repair and come after David. I am not sure David understands the capacity of which Walter can regenerate, perhaps Walter does heal/regenerate himself (it will just take longer).
He then repairs the juggernaut or perhaps finds another juggernaut on the planet. He could easily learn how to fly it from watching the Shaw hologram as that is how David learned to fly them, from watching the Engineer holograms.
As far as why David didnt leave, they could easily explain it as he was busy with his "work" and experiments and wasnt satisfied with the results so he was content there, if nothing else he is flipping crazy, really that could work to. If they can retcon the engineer into being the Space Jockey (which was clearly much larger) they could easily explain a acceptable reason why "crazy as a loon David" didn't leave the planet.
Even though this next movie or next couple movies will end up with just one character in a Space Jockey suit sitting in a chair we must have protagonists. Right now David holds all the cards, all of them and as things are that means certain doom for Tennessee and Daniels. Having Walter racing through space and finding them and coming to the rescue would allow for Daniels and Tennessee to be involved in the next movie, outside of just being lab rats. Then together they could be in the last adventure that leads us up to 1979 Alien.
Whether they are facing off against David and his creations or David as well as Engineers or possibly the introduction of a higher race of beings that the Engineers of LV223 even bow down to.
I think allowing Walter to continue in these movies would allow great themes t play out. Sacrifice, duty, love, what it means to be human, what it means to love, creator vs creation. I feel that perhaps it would be cool for Walter in one final last ditch effort to somehow trap David in the Engineer suit and him be the Space Jockey Dallas and Kane found in 1979. Perhaps while he is sitting there he has a world class monologue/epiphany about creation and humans and what it means to have a soul before he dies. Anyway there are eleventy ba-jillion possibilities but i like Walter coming to the rescue. Plus they made sure the regeneration thing was placed in the viral marketing so perhaps they mapped out something along those lines already.