Lots of heat on this topic, but no real conclusions, as far as I can see.
Which simply points out that ultimately, aliens are a IMTU issue.
Therefore, my take is as follows:
I don't give a damn how many different aliens you have in your universe; what I expect is that any given alien will be (a) consistent with the science of the universe, and (b) internally self-consistent, with explainable origins in game-universe terms. Setting aside the question of the deus-ex-machina of the Ancients, the Traveller major races generally meet those tests.
Most of the BTC aliens can't be decided one way or the other on the tests; there isn't enough information. However, just looking at the portrayals suggests to me that the Ebokin, Dandies, Tashaki, and Viji would outright fail. In GTAR1, I feel that the Sheol would fail; in GTAR2, both the Devi and the Inyx are failures; in GTAR3, both the Inheritors and the Lithkind fail; in GTAR4, the Tezcat and Valkyrie fail. Many of the other races are 'insufficient information'. Note that some of the failures lose because of psychological issues that seem strongly countersurvival.
Taking a liberty, and looking at GURPS ALIENS (i.e., not GURPS TRAVELLER ALIEN RACES x), about the only ones that I can see being portable into Traveller reasonably are those that, unfortunately, would have best been left as humans with variant cultures, rather than true Aliens. Examples that come to mind are the Irari, the An Phar, and the Kronin, but there are others.
In short: Give aliens a reason to have evolved as they did, including intelligence. Also ensure that they have a way to "control" their environment; intelligence and progress will almost certainly involve a desire to do so, and an ability - within limits - to do so as well. Social organization should also be a natural development, but there's quite a bit more leeway there - provided that you don't saddle a race with countersurvival psychoses.