The warp core ejection system needs a major redesign. That thing just doesn't work.
Transporter jammers permanently activated around sensitive areas of the ship; at the very least some areas should be force force field protected at all times.
A major redesign of the computer security on the ships/installations; the system currently installed is just pathetic.
Time travel into the recent past (either by transmitting only information or by teleporting/going with the ship) as a standard procedure in the case of catastrophic failure. In fact, implementing even half the technology acquired during the shows in starfleet.
Mario de Monti wrote:
Regarding the placement of the bridge, I read somewhere that when designing the Enterprise-D, Andrew Probert wanted to put the bridge at the center of the saucer to protect it there. Roddenberry insisted it be put back at the top, mainly as a gesture to other vessels: we´re not here to fight, we´re no warship, we´re peaceful explorers and have therefore no reason to hide our command center.
AKA we're naive fools - believing no one will ever shoot at us with intent to plunder/conquer or just because, despite most major powers in our region of the galaxy being thoroughly xenophobic and aggressive. All that because we're "explorers".