Well, in the original Marathon, just about everything was boxy. Admittedly, this was a limitation of the 2.5D engine they were using, but I actually like the look. I only call those things Nacelles because I don't have a better word for them. I suppose "weapons pod" could work, since that's the other function.
The UESG was never really into "form" either, as we know from terminal information. The CRISTs looked like giant space potatoes*, and the Marathon itself was a converted moon - Deimos Rising in a literal sense**.
Also, the boxiness adds contrast. All of the races in M:Inv have their own distinct appearances. Pfhor are pointy, Nar spherical, Jjaro spindly, S'pht smooth... one would expect at least one of the races to be boxy.
*Start peelin'!
**A "Remember the Marathon" poster is two-sided propoganda. To a Terran, it's encouragement to fight the Pfhor. To a Martian, it serves as a reminder of the UESC's abuses. They were never all that nice to Mars...
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- Dark Side: Gates gives $100m to fight HIV, $421m to fight Linux, Thomas C. Greene, The Register, 11.13. $100m over 10 years to fight AIDS in India; $421m over three to fight Linux. Priorities.