Hello and welcome. Some thoughts/comments:
A Spaceport of our own without being taxed every time we dock. As it stands right now, this $1000 docking fee is outrageous.
You can certainly have one of your own as an independent, you'll just need to build it. There are benefits and drawbacks to either aligning with a faction or flying unaligned as independent. While threat and combat risks are lower with IND, they can have higher operating costs so that they pay a little more for their independence.
There are limitations and a few alternate location options for independent pilots. Fees won't apply until your wealth exceeds 1-million credits and stations in war zones won't generally charge a fee.
No penalties regarding commodities. (We have to make an honest living too you know?)
Not quite sure what you mean by penalties. If this relates to the docking fees, independent pilots may find activities such as mining or recovery a little more profitable at first. They can then hold off on trades until they have a number of profitable options onboard, then pay only one docking fee for a series of trades.
A guild of our own. Sure the Feds and Alliance have their own club to play in, so why not ours? If it weren't for us they'd be stranded with no fuel, or whatever else they need, to fight their pathetic war.
The requested goal of IND was to be more 'off grid', detached from the faction conflicts and faction systems so as to operate as more independent pilots in the game. So for any IND club to form, they'd need to do so on their own as independent operators. That would include building their own outposts and managing their activities independently. They can however, join together for various objectives, just without a required link to a faction.
This last item I partially agree with. The ability to change allegiance with whomever we please, either the Feds or Alliance, depending, of course, on who's winning the war.
Available in Pilot Manager > Modify Pilot.