This is going to be a bit of a meander, but a cogent one I hope...
For me, the rules should derive from the following first principle:
Humans Racing Humans: Human piloted vehicles competing to complete a course in the least amount of time. In the year 2400, they will likely be flying or whatever, but it is still at it's core an athletic and intellectual competition. This means fittest+smartest = you win. All rules should seek to refine/limit the competition to these two areas and filter out as many externalities as possible. In my view, the most insidious externality is money and/or the profit motive. No communist diatribes from me, but at its purest, the goal is to advance the interests human motoring (it is the FIA F1 World Championship!), not make a mint for speculators (ahem CVC) and multinational corporations. But the externalities most relevant to the engine discussion are the homologation and technical prescription rules.
Based on this first principle, I believe many of the current rules/restrictions should be eliminated (obviously maintain safety based rules, except those which entail performance limits). This includes the engine freeze. As a practical matter, you have to honor existing contracts and procedures for rule changes, but unequivocally the engine freeze should be eliminated because It arrests the progress of human motoring. We don't have engine freezes in the auto industry, let's not have it in our motorsport.
Teams should be able to use whatever powerplant they like, with only the lightest of touches on restrictions. A fuel limit (this will result in an emission limit, so no emission limit required). Weight and dimensions. That's it. This would explode innovation and help motoring companies advance human motoring. Teams could use less expensive, older tech in optimized ways to race inexpensively and reliably. We will be entertained. Teams to could use new tech to race test there R&D products. The will dominate and/or fail in equal measure. We will be entertained. Advancing human motoring means facilitating this great sifting of ideas through cost/performance competition. The budget issues will sort themselves out, as the most cost effective power plant solution would work itself out without the rules imposing overly prescriptive technical costs that cannot be supported by the prize payout on offer.
...And as much as I am a Williams fan, I think customer chassis have to be a part of any future equation. Just looking at the Hamilton vs Rosberg battle this year lets you know that identical chassis still provide plenty of fodder for competition. A chassis is no more elemental to the Human vs Human competition than the engine, and we certainly have customer engines, don't we?