The self-learning capabilities of a computer system with a dedicated support staff, enough processing power, and a large enough data set could probably overcome most difficulties with the video encoding itself. The actual exchange of information is likewise solved by the finite means which communication could be passed: there are only so many wavelengths of light, so many types of radiation, so many methods which can employed to pass information from one starship to another at reasonable speeds.
A better question would be why all aliens have eyes, or have cameras, or have eyes and cameras that see in a comparable wavelength to our own. No computer could take raw video feed and translate it into colors the human eye can see if the proper wavelengths aren't in the feed. If encountering a species never seen before, which only sees in infrared, would they design a camera that sees outside of the infrared spectrum? If they didn't, then a Federation ship could only guess at what color the alien's skin is, etc.
Taking the premise that these species want to communicate, it is a good bet they would indeed have cameras capable of "seeing" in many wavelengths. But if they don't have eyes, would they even build cameras in the first place? If they are warlike (Kazon, anyone?), why would they willingly show potential opponents anything which could be analyzed to find weaknesses?
There is the additional concern with all aliens having vocal cords- virtually every species encountered can make noises discernible to humans. A universal translator solves part of this dilemma, as it could filter unheard frequencies to what the human ear can hear and translate the language to English, but only if the alien species makes noise to communicate at all.
Additionally, very few sentient species are not humanoid in the Star Trek universe. This could only come about with planned evolution or seeding planets with common ancestors. I read something about the latter being used to explain the Star Trek universe, but this begs the question of why there are so many superficial differences between species but not radically different ones which could have evolved as well.
At some point, we must realize concessions were made to make Star Trek possible. Actors are humanoid, audiences relate better to visuals than floating voices without video and prefer sound in space despite how little sound can move in the near-void, etc etc. Still, fun to consider.