It's a chronic pain the backside for practically every Wiki I can think of, but I've noticed the "Non-portable Infoboxes" alerts here too. Do you want a hand reworking the infoboxes into a compatible version? I've had a fair amount of experience doing it on the Gundam Fanon Wiki.
Some help with those would be great. I'm not sure when Wikia made the change but I've been hesitant to convert many of the infoboxes since I'm still mostly a novice when it comes to building/modifying templates.
I suggest we leave them as is for now, but instead draft up an experimental version to play around with instead and use a sandbox to test it. That way none of the existing pages get screwed up with and people can keep working on pages.
Fortunately it won't be too hard to create a replacement that seamlessly replaces the previous versions, XCOM Wiki's infoboxes are a tad simpler in what they need to do compared to others I've had to work on.
There is a slight hiccup with the plan, I can put together the basic skeleton of the template, but I can't style it to fit in without changes to MediaWiki:Wikia.css.
The old infoboxes work similarly in that they pull formatting from MediaWiki:Common.css, which was a clever trick by whomever wrote them. However, I can't force the infoboxes to pull code from Common.css, so we'll have replicate and modify the formatting, then add it Wikia.css instead.
How you want to deal with this is up to you, either you implement the changes I write up (simple copy/paste), or you temporarily give me admin rights to it. I don't mind how you choose to go about it, both ways work, no rush.