Ger what you need now based on what you can afford and whether or not it make the cut.
The lens communication protocol changing could happen, but that's most likely what Sigma is doing with the release of a USB lens dock, not to fine tune and adjust the AF of the lens, but to possibly update the firmware if in case Canon does such a thing.
I started on Sigma gear, I briefly went with Canon, and now I'm back to Sigma and no complaints (my Sigma 70-300 was soft, it's AF accuracy was 1/10, but it was fine as a starter lens until the AF completely died). Anyways, it's hard to say whether it's easier to buy third party lenses, because people looked at alternative brands strictly for them being cheaper. Now, they're bringing out gear that holds it's own against the big names, but of course, you spend more money and anything's possible right? The new Sig and Tammy lenses are fantastic, but are by no means affordable for the masses, while Canon is pushing the price of it's new products every time as well, so relatively Sig and Tam are still affordable.
Like with the Sig 35mm, it's not quite "wow that cheap lens maker made a lens that beats Canikon!" but rather "They decided to make a really expensive piece of glass that... no wonder, beats the older lenses".
As for resale value... well, if you're insecure and feel like you will jump over to another system and need to get all your money's worth out of your gear you're getting rid of then yeah. But at least for me, I'm buying gear to use, not eventually sell.