UFO Defense, despite having less gameplay features and slightly less quality in the graphics department, is more satisfying due to the urban environments. I find both of them to be timeless classics. They never get old. You can also edit the hell outta them with OBJUFO and XC2ME2 to change the alien/ship/gun/armor stats. I've used such tools to make the weapons more realistic and pump up the stats on some of the weaker enemies. Makes for a very rewarding remix.
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The Lobstermen in TFTD scare the shit outta me.
They're very menacing.