About the only thing bad about the (E) is the OP reduction and maybe dissipation. Large energy reduced to medium is annoying, but with Heavy Blaster available, the main thing lost is the shot range. As for missile slot, that is a classic case where if I do not have enough OP, it gets left empty. If I do not have Locusts to spare, I do not even waste the OP on large missile for Apogee. Actually, medium missile means I can mount small salamander or 1 OP harpoon or sabot. I cannot do that with a large mount.
Want to really weaken Apogee, weaken the shield. Odyssey took a big hit (to the point it cannot tank anymore) with the shield downgrade. Apogee would too.
For exploration, you want more crew to survey (and then colonize) planets, not less. Probably just reduce skeleton crew, but not max.
The Apogee as it is is already close to being an explorer ship due to how mediocre it is in combat now (to the point that I do not think about using it) and the builtin mods (even if relatively insignificant). It can have more capacity all-around, and it can be useful for its intended purpose (of exploration).