Where's the option "I don't care either way"?
To be honest, I don't use any of the Mint tools, besides mintMenu. For me, apt-get easily replaces mintUpdate and mintInstall, although I occasionally still refer to Synaptic from time to time. However, I support the concept of giving the user as much control as possible, even if it complicates things, so I'm in favour of giving mintInstall users the ability to access all the packages available in the repos, directly from mintInstall. I'll leave the exact implementation of this to Clem and his team of hard-working developers.