"... making a mashup between two games ..." mean one of three things to me:
a) You're trying to create a multi-cart that lets you pick which game you want to play: run Crystalis (MMC3) or Metroid (MMC1) or Castlevania 2 (MMC1)
b) You're trying to create some kind of combination game (read: insane romhack) of all 3, which means actual detailed reverse-engineering of all the titles involved,
c) You're trying to create something brand new using these games' assets.
If it's (a): yeah, you're in for pain unless you can find a mapper that supports both MMC1 (no additionals) + and MMC3 (w/ battery-backed 8KB PRG-RAM), thus may be forced to do what's described in (b),
If it's (b): you don't need some crazy mapper that can do both: you need MMC3, and you get to convert the MMC1 games to MMC3. You're going to have to do some form of this anyway to deal with the fact that Crystalis is CHR-ROM and Metroid is CHR-RAM,
If it's (c): pick whatever mapper suits your needs / minimises your pain of development (and expect to be DMCA'd by Nintendo for using their assets in Metroid -- yes they are watching).
Have you done romhacking before? Have you done NES work before? This is your first post, so if I seem apprehensive about it, hopefully that explains why.
P.S. -- Absolutely none of the games mentioned
for mapper 116 are in BootGod's database. So knowing whether or not they can work with battery-backed PRG-RAM is... well... you're putting a lot of faith/hope into something with no guarantee, IMO. Better off sticking with a known/familiar mapper.