As it concerns base sound quality, I think the JV-1080 sounds better. That said, I think post-processing is the norm with most synthetic productions, so base sound quality may not be that strong of a determinant. I find the modern Proteus-engine machines to work very well with pedals and rack processors in that they provide a sound quality that lets post-fx shine. So it depends if you want the warmer and thicker tone of the Roland or the thinner, more precise sound of the E-mu.
As it concerns MB after expansion, yes, it is true that you have more available with the E-mu. That said, I think Roland does a better job with less memory. The E-mu is more suited to synthy sounds as opposed to the Roland, which can do a better job of ROMpler tones.
As it concerns deep programming and potential in the engine, the E-mu is clearly superior given its real-time matrix modulation.
The desirable ROM expansions for the E-mu can be costly in the current market.
The Roland is a capable machine to be sure, but if not programmed well will sound like the 90s.
To be fair, to answer this question also requires some real knowledge of your working style, other gear, and other things not related to the gear at hand.
Just so you know my bias, I do not nor have I ever owned a JV-1080, but I do own and love a Roland JD-990. I have owned a handful of modern Proteus machines, and currently I own and use a XL-7 with 4 ROM expansions, as well as an older UltraProteus.