Lightning (FFXIII) vs Lenneth (Valkyrie Profile) - most badass female JRPG protagonists, both have long and short range weapons, they both have an issue with their gods
Jeanne (Jeanne d'Arc) vs Dart (Legend of Dragoon) - both swordsmen, and both have another form (dragoon and holy armor)
Rand Travis (SRW) vs Asgard (Wild Arms) - Asgard is a golem, and in a couple incarnations he was a giant mecha. Rand Travis is part of a repair service company, and uses a giant wrench, with some smaller wrenches he can throw or make wrench-chakus with.
Sophie (Tales) vs Scion (The Bouncer) - Both are fist fighters, Scion can fight many mooks and robots to save his girlfriend who is similar to Sophie, in that they aren't normal people.
Pale Wing (Global Defense Force) vs Chimera (Resistance) - Pale Wing fights aliens that have giant bugs, UFOs, huge mecha, etc... Chimera is an alien. --- http://i49.tinypic.com/161f693.png