I think the transponder is way too overpowered. If I turn it off, I can go around literally everywhere even if everyone hates me. If they stop me and ask me to enable, all I do is refuse and leave and I get negative rep, which is already at -100, but it makes no difference. I can plunder and loot to my heart's content, the only penalty is that I have to wait 3 months if I raid things nearby a base/planet, but other than that no one identifies me as the enemy, no one chases me, and most of all there are no serious reinforcements coming after me.
During the colony missions, I liked the idea of having a bounty on my head from tritachion, but unfortunately they are scripted, so if you avoid/break their triggers they get canceled and you never see them again. Maybe having bounties from the factions you mess with (-50 reputation) they send all they can after you, making movement tricky (unless you have stealth ships, and even then if someone spots you in their radius, all hell should break loose).
I'm still waiting for exploration to be more engaging, and less of a click fest to scan planets. That part is really not fun and there is really little incentive to do it.
The Ludic Path needs a bit more love, so far their missions are quite sparse, and for some reason they are neutral with the pirates but they mostly give you bounties to hunt them. I think they should give you bounties for the other factions in the core sectors, just like the pirates do. They also need more Contacts, especially for commerce.