I don't think there's going to be another Advance Wars.
Intelligent Systems is an incredibly talented bunch, able to do something Nintendo is struggling with at the moment: putting out medium to high quality games at a high frequency.
They have roughly the sames manpower as Retro Studios, but are putting out more than four times as many games, without even counting their DSi games.
Their only problem is that their core titles don't sell. The DS Advance Wars averaged less than 500k, and the DS, GC and Wii Fire Emblems sold just as bad. WarioWare saw a dramatic drop in sales toward the end of the DS, largely because the microgame genre is becoming crowded by free smartphone games. It's just not the series it was anymore.
Before the 3DS, Fire Emblem had been in decline since 2003, Advance Wars in decline since it started, and Warioware was starting to die as well. Paper Mario was doing well, but that was their only series doing well.
It's clear Nintendo told them to shift their course. Fire Emblem - Intelligent Systems' golden series - was to be cancelled if Fire Emblem 13 didn't sell well (source: http://serenesforest.net/forums/index.php?showtopic=40303&page=1). Warioware became a download only series, and downscaled somewhat. Intelligent Systems started making a lot of DSi games, and then 2 3DS e-shop games (Crashmo and Pushmo, both highly successful).
Intelligent Systems changed course somewhere around 2010. They either had to manage to make their series popular again (which they did with Fire Emblem), or abandon them in favour of making new IPs. This most likely lead to the death of their least popular major series - Advance Wars.
There most likely won't be another Advance Wars.
