Get some money and buy 1 reasonable ship.
Get to Segaris and harvest the freelancers for $$$ and move into one as they seem to be the best balance of ship (shield/turrets/weapons).
Taking down freelancers give no loss of Reputation.
Get up to Argon space and swap out 2 of the 4 guns with shield killing guns to help harvesting capital ships.
Set up turrets to "attack missiles first".
Get some marines with a varitey of skill levels into any ship (I use some frigate as its a big investment in these guys).
Now you are ready to take down Caps.
Start a few haulers in Nopileos Fortune II (above Pious Mists II) to get you marnes skills up even further (easy captures).
Nopileos Fortune II give no loss of Reputation.
NOTE; Scale Plate are a good target as no one likes them and you generally don't lose Rep wherever you kill them.
Now to take down the big Mil and XL ships in my freelancer:
- I get in behind a capital ships arse (very close) and take down the engines and STAY THERE!
- I then pick off any back facing pop gunes.
- I then "pop up" or "pop down" and take out all the other guns/turrets waiting for my shields to recahrge as needed and popping off drones and laser towers as needed but STAYING close and behind the dead engines.
- Once all weapons are down I either take down the Main Shield Generator, or leave it alone, and then take shields to 0 and hull to 75%.
- I then scan and board and select the marines from my transport that was follwoing me to take the target over (Works for any capital; but military takes better/more marines.)
- Get in suit and reapir the capital to sell for $$$ or keep to add to your anti Xenon fleet.
NOTE: if you lose Rep and want it back; sell a load of energy to a station ONE AT A TIME... it's time consuming but it works; try it... if you rep is too low to land on a station then, as there is no diplomacy, then you have to GRIND out killing criminals near their station, do mission, or just kil them all

Latest 7 patch is mainly unchanged; there may be a couple of fighters to take down protecting the Capital ship; but they are usually weak/stupid and can't aim.
BUG
Latest patch has added the "bunny" capitals.
If you are too cloase (maybe in the bandbox) then sometimes they dissapear and reappear somewhere else.
This is an annoyance... and is seems the devs are trying to help against stuck ships...
Patch Ideas:
OMG; please ease the transfer to stock from "for build" and "for sale"... this is a nightmare at the moment where you have to shuffle the items using ships ON THE SAME STATION.
Diplomacy - It's been so long that you have grind out increasing rep with people you never even shot in the first place (looks sideways at Devs here) as if your ships/laser towers hit ships you lose rep (seeming there is less now) - this can/should get you embroiled in wars too... and there is nothing like betrayal to rock the verse up a bit

Spying - It seems we can have plenty of opportunity for this - for various nefarious reasons; including stealing tech (blueprints) etc.
Harder to Capture some capital ships - harvesting the build ships is just too easy!.. 1 fighter and a covrvette full of marines get me 20+ mil...
"Wonders" - a little bit "tacky"; but building these can give you a boost - just dont go overboard.
Academies - to invest in training marines.
Rebellions - add in some for of happiness so that planets/sectors can revolt if they feel unloved (too far from the empire and not supported enough with food/luxeries etc.)
... thats enough off the top of my head.