At the risk of violating my own IRL about Battletech rule...At the risk of being a party pooper (and I'm pressed for time at the moment so couldn't check to see if it's already been answered)
1. Why would any House formally ally with a 2-bit merc unit? While they're chucking Regiments around and generally shifting their weight in tectonic scales... we never put more than a lance on the field. We seem like awfully small fish, more of a Spec-Ops unit at best rather than someone they'd want to be hanging posters of on their walls. (consider this an oblique plug for putting more controllable units on the field)
2. Maybe some kind of curve for rep gain? Basically, if no one knows me and no one really likes me... they all kinda shrug if we take missions against them. Sure, our employer likes us but it's not something everyone takes note of. Later on though, when we've got the House Marik cheerleader squad sending us love notes, THEN their enemies take note of when we show up to blow up their shiny stuff and as such, start to shake their fist at us.
And I've managed to lose my train of thought for the 3rd idea/question. Getting older sucks!
The Factions are not aligning with us... we are aligning with them. While this may seem a minor point it is supported in lore.
We are small fish. No doubt. We are also operating in the Periphery where even 1 lance of moderately unsuck Mechs will make a difference. With FLASHPOINT/CAREER mode our 1 Lance deployment per fight becomes more interesting.
Ahhhhh... Spec-Ops... frankly this is what we Mercs are here to do. Timely, precise, no politics, deniable... Darius even mentions as much a few times.
Only around 1 in every 20 members of most militaries will ever actually fire a weapon at an enemy. (Yeah take a moment to wrap your head around that)
Of the above group only about 1 in 5 will actually hit anything.
If however you are a member of the "spec-ops" groups... the above odds sky rocket! Instead of just the above 1% roughly speaking 2% will have actually been fired upon and actually fired back causing a hit.
( I know maths has occured )
Actual Trigger Pullers are rare... unless you are Artillery (teasing @Prussian Havoc )