Using AE rules, heavy ships (at least light cruiser) are definitely more resilient than smaller (frigates and destroyers). Usually, the former have a lot more of everything, except maybe engines, whilst the former will usually have a low armor value. Even with powerful engines, they don't last long on a table unless you keep them out of reach, but then, as they usually have short range weapons, they are just lost points. Usually, when I take small ships, that's for two reasons. Fun, but mostly because I still have some unused points.
So, unless designing a fleet with a lot of small (1 hull), unarmored and lowly armed (one weapon only) ships (a lot of them!), it is usually more interesting, IMHO, to have heavier ships. Note that a ship with an armor value of 5 is much much more expensive than the same one with a armor value of 4 (normal, it can be near invulnerable).
Also, beware of creating ships 'too powerful and too armored'. It could kill a game. But that's just my opinion.
BTW, what do you prefer, play with existing universes created by you or other people, or create your own fleet versus a fleet created by you opponent?
Marc