I love this idea! My only suggestions would be to use widely available units so that players of Faction X won't be left out because their nation doesn't get half the box. Another idea would be to exclude mechs from the Intro Box, so that new players with just that don't have to buy duplicates if they don't want to.
I'd duplicate as little as possible, even in the factional ones. Drop one of the Regulators for a 3058 Vedette, Brutus, or Zhukov. This exposes the players to as many new minis/designs as possible, improving the odds that they'll really like one(or more), and buy more of that mini(s).
Ditto x2
As much as I like my 4 Ontos, or 4 Guillotines, or 4 Stingers, or even my 16 Savanah Masters, for when I want a "Pure" lance.
I much prefer the idea of new players getting singles of everything to diversify selection & options to play.
You can also get "factional" feel w/o being all "super specialized".
For instance, using say House Liao for example.
A Raven, Cataphract, Victor, or Pillager all offer a feel of Liao while 3 of them are on the Faction lists of other Houses. And none of them duplicates the Vindicator or Catapult of the main boxed set. (Not that Multiple Vindi's is ever a bad idea for Liao IMHO)
Meanwhile a tank unit of Po/Regulator with Vedette, Maxim, & Condor/Minion is a solid Liao mix but also offers generic &/or widely delpoyed miniatures too.
An infantry selection of Foot Plasma Rifle Squad, Jump Infantry Squad, Standard IS BA, & Fa Shih also gives it a Liao feel while leaving plenty of room for other faction lovers to pick it up as well.