Yes, a class based skill tree system is not really fitting the JA setting. OTOH by choosing mercs with different traits and stats you already do some specialisation within your teams. So why shouldn't somebody skilled in handling heavy weapons learn things associated with this better and faster than anything else?

So, IMO, a skill tree system where not every merc can improve in every field is not a no go in my book.
A combination of classes (sniper, mechanic etc. ...) and learning by doing (as in JA2) would IMO be best: A merc learns fastest and easiest in things related to his class but can still train in everything else (tho not to masterhood or slower or something).