You can still do the Black Omen and get the ending from fighting Lavos in 1999. Once you beat his first form (Black Omen) and get inside him, his shell has a save point and a gate back to the End of Time. After that, just use the bucket and you'll still crash the Epoch into him which nets you one of the two main endings.

Yeah, its possible to steal enough Prism Dresses to outfit all three girls (Ayla especially needs it) so this is why I usually do the Prism Helms instead but that's what New Game + is for.

Like VeloZer0, I feel Marle doesn't have much end game appeal. I usually use Frog and Robo cause I prefer maximizing my turns. My only recommendation is to build a party with characters that have great single attack techs. It helps alot in the final battle and it gets rid of annoying pests like Lavos' appendages in record time.

Honestly, just go through the Black Omen for the great gear and pick up a few Tabs. Of anything the levels you will gain in there will probably help you beat Lavos pretty easily without the added gear and stat items.