1) Probes: It would be great if you could assign missions to probes, like 'search stars', 'concentrate on FOW', 'FOW around my planets'. Things like that, nothing like wondering why your probe heads off to the middle of nowhere that you will not care about for dozens or hundreds of turns.
2) Main map search, trying to find untapped resources has me searching for small hard to find symbols so I can send constructors. Or having to search by eye trying to find the last few anomalies sinc these do not seem to have symbols.