Of course there should be also structural means to discourage RTS (e.g. encourage players to produce and use LESS military units, so they will make their moves faster, or simply some "gentleman agreement" which is always quite fuzzy and difficoult to agree)
Anyway, this is my contribution: the proposal for the FREEZING BUTTON:
FREEZING BUTTON - Did anybody think about a "freezing" button? You can push it to ask the server to "freeze" one (or more) selected player(s). If he doesn't answer inmediately to stop the slow freezing process (which takes say 60"), he will be frozen for a max of 10 minutes.
When frozen, he can do everything except moving units, any unit. You can then safely perform your attack, but after 120" in the frozen period, he can already push the "defrost" button (which takes another 60") which will hurry you to finish your attacks. So you have at least a minimum of 3' to perform them.
LIMITATIONS FOR THE "FREEZER" - You can freeze the same player only once per turn. Freezing can't be performed around TC (1 hour before/after, or <10h since last time freezing was performed for that player- to discourage TC moves), or when the other player is freezing a 3rd one. You can freeze as many players as you want at once, but you can't freeze them consecutively (you have to wait 5 minutes between each freezing sessions). This will allow enemies to freeze you instead.
Same for the frozen player: enemies have to wait 5 minutes between each freezing performance against the same player, so he can start freezing them instead.
WHO YOU CAN FREEZE - You can only freeze players with which you have contact. You can't freeze allies. Frozen/freezing status of players will not be shown to 3rd players.
DISCOURAGE IT - And there should be also some cost, just to discourage freezing, but I can't think which type.
CHEATERS

I think it could be relatively easy to implement it.
A special message type, by default "pop-up", should be added: "Moving related system messages"
A new window type "Freezing" should be implemented, with a table of all known players, along with 2 timeleft/progress bar for both their FREEZING and FROZEN status.
SOFT VERSION - Maybe we can experiment it with a "soft" version: the frozen guy movements are not blocked, there's just a banner who "invites" him not to move units, or that asks for confirmation before performing them.
A DIFFERENT APPROACH: IMMUNIZATION - An easier option could be the immunization. You can ask once per turn for a immunization (10 minutes) during which you are immune from enemy attacks, and can perform your attacks with ease. I would not let more than 10 minutes cause some well coordinated guys could immunize consicutively and "defend" cities with stacked international units. To limit this, the immunization could also be preceded by a "infection": a randomly-long period (from 0 to 50% of immunization period) in which you can still be attacked, giving a small window to perform attacks against multiple-defended cities or stacks.