Suikoden are games of there own combination that is not really re produced in any other games that I have seen (3 and 4 are good but you do need to get used to the new graphics 5 I don't think I played through, it is something to go back to though I guess)
But I also loved the Shining Force Games (start out on Megadrive/Genesis) Shining Force 1 and 2 (SF1 has a remake for GBA), the 3rd one is for the Saturn and comes in 3 parts and a premium disc (there are also a bunch of side games that have no RPG parts, pure strategy games, Shining Force CD for the Mega/Sega CD and Shining Force III for the Game Gear (Shining Force 1 and 2 for the GameGear are the first 2 Stories in Shining Force CD, the CD has 2 extra ones as well though))
Asides from the side story Shining Force games the main series is a mix of RPG adventuring (exploring towns finding items talking to town folk to progress the story and find extra players, a bit like suikoden) and turn based strategy battles (using up to (I think it is 12) hero's in the battles) there is not 108 of them though

but there are hidden ones, Shining Force III is a much bigger game to the 1st and 2nd one so there are more characters, not sure on the grand total though (the first 2 parts of 3 tell the same story from 2 different armies point of view, the 3rd part brings everything together and continues on from both 1 and 2, the prem disc is just bonus stuff but you can use your final army to fight through extra battles on that disc)
The side story games are much the same as the main series but instead of exploring towns ect you are just told what you are doing between battles but there is a shop ect, during the battles you can find hidden items and new hidden heroes to recruit (usually 3 hidden heroes through each of these side games) the rrest of the heroes join regardless throughout game play
P.S. Shining Force III [Saturn] (all discs) are translated from Jap (only disc 1 ever had an english release) Shining Force III [GameGear] also has a translation done (the other games are english anyway [the gamegear SF1 is jap but as that is part of Shining Force CD])
The megadrive ones should be playable on DS (PS2 they are not, the first one has a bug in the PGen that was never fixed and stopped the progress of the game)
Meh as you are emulating anyway... I don't know why you are limiting yourself to 2 consoles so I will re-list the games
Shining in the Darkness (Megadrive) [it is not the same type of game it's dungeon FPS type RPG] [You may not like that game so just jump to the next one

, it is not a game that needs to be played]
Shining Force (Megadrive and GBA) [GBA version features extra game play and improved graphics]
Shining Force II (Megadrive) new story but does has very minor references to the first one
Shining Force CD (Sega CD) 2 short stories plus 2 extra ones
Shining Force Gaiden 1 & 2 (GameGear) these are the first 2 stories on the CD version above (these do continue on from each other, after SF MD and before SF2 MD)
Shining Force Gaiden III (GameGear) [Translated] this story is just before SF2 MD and after SF MD & SF1/2 GG (it can be played without spoiling the SFCD/SF1/2GG)
Shining Force III (Saturn) it's 3 games [Translated] the first one was english anyway but parts 2 and 3 are jap only but have a translation as does the premium disc (the prem disc is silly hard though, but has no real story it is just bonus battles, still fun until it is silly hard so the first few battles are fine it's only the last few that are silly hard)
There is a game for the PSX that has very much the feel of Shining Force but is a pure RPG so no stratagy battles (it is by the same developers as Shining Force so it's not a shock it has the same feel to it, I forget the name of it at the moment though)
There are Shining games for the PS2 & GBA (asides from the Shining Force remake on GBA) but the game play is Action RPG rather than the original strategy that fans come to love, there is even a Shining game for the NDS but is Jap only and yet to be translated
Most Sega consoles are emulated by Fusion aka Kega Fusion up Sega computer systems (pre mastersystem/gamegear) up to CD-32X games (actually Fusion is the only emulator to support CD-32X games)
Saturn is emulated best with SSF
a great strategy game is on a less known system called the NEC PC98 (a japanese computer system) the series is called Farland Story, parts 1 to 6 are fully translated to english (that 6 games not 6 parts of 1 game)
I don't remember the exact emulator I used for those mind off hand there are a few PC98 emulators around (I possibly used Neko Project II though, but at the time I was testing all sort of emulators for that system)