If I wanted Systems Expertise for faster jet recharge, it would be more likely for escaping swarms. Guardian is vulnerable to getting swarmed by a mob of fast ships. However, chasing ships down is still good against the cowardly AI. Chasing cowardly ships until they get cornered is annoying. Aurora is faster than Medusa, but it still take some time to catch up, and Guardian is slower than Aurora.
As for tier 5...
Systems Expertise would be good if player wanted to pilot other automated ships (but player who gets both Tech 5 skills will likely pilot the capitals).
Missile Specialization is probably irrelevant for Guardian that still has unlimited missiles, but if that gets stripped, then Missile Spec. would be good.
Best of the Best as Spec.Mods successor needs no explanation.
As for the new other Leader 5 skill, since Guardian will probably cost a huge lot of DP, stronger redshirts probably means little if there is not enough DP left to deploy enough extra ships... unless Guardian costs so much CR to deploy (like Ziggurat) that it cannot chain battle, and it must sit like a hangar queen and let other ships fight successive battles (kind of problematic in a red system with several multi-Radiant Ordos after your fleet.)
Hull Restoration is to make inevitable deaths less painful when your stupid AI ships blow themselves up (or reckless player gets in over his head). For players who give up combat power for QoL.
No comment on DC.
P.S. I have not tried this, but if Ziggurat costs so CR to deploy, then perhaps an easy way to kill it at Alpha Site is to deploy some ships then retreat a few times to drain its CR, then fight it while it is crippled at zero CR. If that works, and Guardian gains massive CR loss per deployment as a balancing mechanism, then Guardian losing too much CR from deployment might make it a lame boss if player catches on.
P.P.S. My point was if player goes double tech 5, then he only gets to pick one other tier 5 skill, so no munching with multiple non-Tech tier 5 skills. BotB would probably be the likely third pick, though.