One of the problems Xenonauts might run into is that proposed retail 30-40$ price tag, especially if the new release of X:EU is bundled/accompanied with 2K Marin's "XCOM" (don't even get me started on everything wrong with 2K Marin and their contrived and generic FPS "reboot" of a legendary franchise) within the 50-60$ range. One of the advantages for buying indie games, especially over digital distribution such as steam, is that they're usually significantly cheaper than AAA titles and often offer more bang for the buck when done right. 30 bucks might be a steep for many, especially if 2K/Firaxis decide to release the title at a price like 39.99.
Also take into consideration that Firaxis is a known and established company that has a reputation for being very faithful to IPs (not to mention all of the marketing funds they have at their disposal). They're making use of the actual license - not a clone, spin-off, or 'spiritual successor', such as games like UFO: Extraterrestrials (another spiritual successor that in many respects just ripped off X-COM with little innovation).
I personally feel Xenonauts has a lot going for it in terms of setting and direction even if it is lumped into the category of 'XCOM clone'. But, depending on how X:EU turns out, there may be quite a few folks (purists or people new to strategy games) who decide "Hmm...why bother shelling out the cash for a spiritual successor to XCOM, when there's an actual XCOM title being released?" Retail price and more importantly the timing of the release are going to be pretty important factors here.
Oh, and of course the more coverage Xenonauts can get from big game casters like TB and the Yogscast, the better. The popularity of these guys ensures that even if a game is rubbish, its going to get a lot of attention. Just look at what happened when the Yogscast livestreamed X-COM earlier this week - a lot of interest was generated and sales for the X-COM bundle increased considerably. Even todays Steam deal has the X-Com bundle on sale for the front page. This kind of coverage can't be underestimated, and it truly helps offset the fact that indie developers don't have millions of dollars to toss around for advertising like the big game studios.