No, it's a valid issue, but you have to put it in perspective of the size and lifting capacity in relation to the engines.
The engines on the pelican are honestly incredibly small for providing so much lift, and are rediculously fuel effecient if they can also boost into orbit(take a look at the fuel 'effeciency' of the Space Shuttle to see what I mean)
Just by what you see in the game, it's a lot less impressive untill you really grasp the scope of what it can do considering it's size. It can life up to 70 tons, which would be approx. equivalent to 70 or so normal cars nowadays.
While it could go with less fuel to reduce the size, you have to imagine what kind of missions this thing would go on. Mid-air refuelings aren't very valid when you're trying to orbital-insert a bunch of marines without anyone noticing, etc.
Also, there isn't quite as effective a fuel system 'by-gallon' as jet fuel and whatnot. Sure they could theoretically use fusion engines to power the things, but those are big enough to power a battleship, would be well out of mass-production cost-range, and remember, the smaller you make something, the more expensive it is. The micro-fusion core powering the MJOLNIR was insultingly expensive per-unit, if I recall. So sticking with a somewhat unwieldy, but easy-to buy, replentish, and aquire in large ammounts, fuel would fit a lot better for more mass-produced units like the pelicans.
In regards to the 'Pillar of Autumn Connundrum', if I remember right, it wasn't so much 'it doesn't fit, but we don't have time to' it was more 'sure we can make it fit, but this is a *lot* more fun', and as that's the point of a game, I'm willing to let it slide just this once