The real trick to developing them, it seems to me, is that you need Guard before the bash teams spam it, and you need Tackle before the finesse teams get Dodge. But because they level so slowly, you're behind the curve most of the time. Fortunately the rookie team is naturally pretty good against rookie bash. As a result Khemri's record in bash-heavy TV-matched leagues is quite good. But if you run into elves often, optimizing for control (which I think of as Guard, plus Grab/SF later) will not help you as much as Tackle.
Which I suppose is why people recommend MB early: it has the virtue of being effective against both bash and finesse (plus it helps you skill faster). It's unreliable against av8+, however, and vs av7 you have to catch them first, which vs ag4 is not easy. I much prefer to play with Guard on my TGs, but MB seems the better long-term choice in theory. (If Plasmoid recommends it, it must be right!)

On the other hand, if you embrace the idea of inducements, a slow-developing team is perhaps a virtue. Khemri are, as you say, a lean core roster, and in a developed perpetual league environment you will be behind the curve more often than not. This is another factor in favour of Guard, since Guard limits his advancement (and cost) for the foreseeable future, barring lucky MVPs. A Setekh or Ithaca, or especially bribes, can really help, and you can plan your development around them.
Re: fouling. If it's true that Khemri need to control via player-removal as well as via positioning, it's clear that they need not only the MB but also solid DP and fouling skills as well. Fouling's tricky on a control team, though, because positioning and man-advantage are both so very important. Here's where I'm not sure Guard is a good doubles choice on skeletons. Guard puts them in position to be hit next turn, which substantially shortens their lifespan. Sneaky Git enables them to foul without needing to disrupt your "red rover" line to get the assists. Less reliable, yes, but you can get a boot in every turn, without as much fear of going down a man. The problem is skilling that SG up to DP later, which seems like it would take forever without an explicit plan to force TDs with him. Bit of an adventure, but SG/DP would be a very nice skellie imo. Plus, if you like 3 skels on the LOS vs bash, you really only have space for 1 more (assuming you keep a Throw-Ra on the field, which is a good idea for the SH), and since a mobile DP skel is a requirement, doesn't the Guard skel end up on the line a lot? I'd rather he not be there....
We'll see how it goes, I think I will continue to take as much Tackle as I can in order to shore up the obvious Elf weakness this season, and try to focus on honing my fouling game. Tackle also has the interesting effect of routing your dodgy opponent to where you want him to go -- Elves hate that skill! Ultimately Guard spam plus fouling is probably where I'd like to see the team go, but that depends on TG survival as well as some lucky Skeleton casualties.
But there really is no good answer. Strategically-placed Tackle and Guard combined with a smattering of MB and DP strikes me as a solid diversified build when presented with such uncertainty. That, and roll 10s...