Were the senshi goddesses during the time of Silver Millennium? 

I'm curious given that we do have a hint of that with Queen Serenity's role on earth. 

However this came to my mind concerning Sailor Jupiter's non senshi abilities. Rather than being a Jupiter/Zeus, Makoto comes off more like an Athena/Minerva. 

Is this the case with the remainder of the senshi?

Much obliged.

God bless.

During the time of the Silver Millennium, the senshi were princesses and the strongest warriors of their respective planets. This is obvious via the fact that they each have their own castle (as stated in the manga). I think we also get proper confirmation in the manga that they are indeed princesses.

For some reason, the Moon seemed to hold all the power in the galaxy, hence why we get the other princesses protecting Princess Serenity. That's what always baffled me, the Moon being the most influential? I mean it's not even a planet?

Serenity didn't actually have a senshi form back in the times of the Millennium. I think we only get to see her reborn as Sailor Moon is either because Luna got confused and reawakened her as this non-existent Sailor Moon persona or because they needed the strength of the princess as a senshi. Naoko left so many questions unanswered, which is what a good writer does. They leave us space to think for ourselves.

However, didn't Queen Serenity desire for Princess Serenity to come to be a senshi in the future? At least that is my understanding from Crystal (and by extension the manga I assume).

Also, are we sure that Queen Serenity didn't previous encounters with Chaos in the pre-Silver Millenium era? Didn't she wield in the moon stick/wand in such a way that allowed her to do what Usagi does in the future with the wands?

I have a related theory here: http://www.thegalaxycauldronforums.com/t9965-sailor-avatar-incarnations#282314

Queen Serenity might not have been a senshi herself either, she may have just been wielding the power of the Silver Crystal through the Moon Stick. Sailor Moon seems to have more variety in her attacks though,and doesn't have to use the Silver Crystal at times. Moon Tiara Action and Moon Gorrgeous Meditation use other things for example, so I doubt Queen Serenity could replicate them. I think making the princess a senshi made her stronger overall, as her powers constantly evolved over the series.

Back on topic, maybe the original senshi (like the very first Mercury, Mars, Jupiter, and Venus) were similar to goddesses, but I think the ones we saw towards the end of the Silver Millennium were not. The people of Earth might have thought of them as goddesses though, but they were just powerful in comparison to what they were used to. Their Sailor Crystal's power might have diluted over the years and years, while the Silver Crystal remained strong, explaining why there's a clear hierarchy between the Moon and the other planets. Dying and reincarnating might have reset that though, so the senshi could potentially be far stronger in Crystal Tokyo than in the Silver Millennium.

I never got the Athena/ Minerva vibe from Makoto though, she always seemed to be electrically centered when in civilian form, which points me to Zeus. If anything, Ami fits Athena better, though she's more of a combo of Athena and Hermes with her technology skills and battle planning.

But Makoto also has aspects which correspond to the lesser known facets of Athena. Namely her more domestic abilities and her defending the weak. Ami may have more of the classical knowledge/wisdom aspects of Athena, but I think that may actually go hand in hand with Hermes/Mercury as well.

Makoto demonstrates both a gentle and rugged side distinct from all the other senshi, rivaled only by Haruka.

The daughter of Zeus facet drives the point home even more.