Mongoose Traveller is very generous with skills compared to Classic Traveller - you can get quite a lot of them during character generation. Beyond that, adding too many "pluses" to your 2d6 roll is not a very good thing. The easiest way to deal with experience in Traveller is to give the characters a few skills (1 in CT, more in MGT) per 4-year "term" of gameplay to match the rate at which your character gains skills during character generation, but even then, keep in mind the old limit of total skill levels to INT+EDU.
Also each skill point MATTERS. This isn't D&D 3.5E where a "+1" is 5% on a linear 1d20 roll - in Traveller a skill of 1 is very influential on gameplay and a skill of 3 is very powerful. A skill of 1 is a major employable skill - with Medic-1, for example, you can find a job as a medic aboard a starship. A skill of 2-3 is a proper professional skill level. How many employable skills, let alone proper professions, can a person have at once, especially with average INT and EDU? Not too many.
Your average starting MGT character is not the equivalent of a level 1 D&D character, but rather of, say, level 6-12. The character is in his or her prime and is a skilled veteran. There is not much room, or need, for much skill development beyond that.
So how to handle character development other than above-mentioned 1-skill-per-4-years? Let them earn contacts, amass wealth, gain political power, advance in SOC, pay off their ship's loan, pimp up their ride, buy additional ships, establish a trading company/criminal gang/mercenary band and so on. In short - advance in the game universe by their actions.