I have been trying thoroughly, THOROUGHLY, for weeks to get an imperium playthrough going in nexerlin, and it just doesn't work, there just doesn't seem to be anything there to use, you can't fight any speed or frigate based faction for obvious reasons, which rules out the pirates, luddic path, and roughly half of the mod factions, you can't fight any of the offensively focused factions because it's a slugging match you won't win, which rules out everything else.
Don't get me wrong, when the Imperium ships work they work beautifully, and I even made some good headway into the IBB in one of my attempts, but they always end the same way, me dying to an otherwise easy fleet because of my complete inability to choose when and where I'm even willing to engage, never mind where I want to, and heavy flux inefficiency of my ships due to expensive weapons and poor shields.
Honestly I'm just gonna have to say that an even predominately II player fleet is not feasible unless you can fill up half your 35 ships cap out of the gate, and honestly I find myself simply passing up II ships (except the Lynx) when I find them, unless I'm looking to try something silly that almost never works, because they just become such a liability in mixed fleets due to the below average agility and the resultant inability to effectively disengage and reengage as needed without the support of a large II battle line.
Now there is one thing I haven't tried yet, because going all into the combat skill tree with the emphasis on high OP weapons and fleet tactics seemed like a poor choice, but I'll have to try that when I get back home next week, trying to get this running now has eaten up many hours of persistent failure and humiliation.
Edit: you know maybe I'm going about this wrong and it's not the Imperium who suck early on it's the starter fleet Nexerlin gives me, though I didn't have any luck when I totally replaced all of those ships either, I don't know. I am thinking the Malleus is probably a bad flagship for a fleet of 3, and the basilius is just invalid 90% of the time.