A point that a lot of people seem to miss is that market prices aren't just affected by your transactions, but the transactions of every empire in the game. An AI empire selling minerals (for example) will lower the selling AND buying price of minerals for every other empire in the game, including the player, and vice versa for buying. This means that the price points of the various goods on the market is unique to every playthrough, emerging from how much of which resources are produced by all empires, AI and player. What OP is pointing out is evidence that it would be smart in OP's individual playthrough to produce food over energy, not of a fundamental imbalance. In my first playthrough the price of both minerals and food rested around 0.7 per unit. In my current playthrough both sit around 1.5-2 per unit.
Even if there was a fundamental imbalance that made building generator districts less efficient than generating more trade value or producing other resources for sale on the market, I don't think that necessarily means generator districts need a buff. Whereas trade value can be stolen by pirates and selling on the market leaves you vulnerable to price changes, energy from generator districts is 100% secure (unless the planet is lost) and the jobs can be worked by any pop in the game except pre-sapients, so imo it would be fair if making EC through generator districts was a bit less efficient than alternatives.
The infinite credits market exploit is already fixed. The other 'exploit' you complain about (stockpiling resources to repeatedly sell at baseline rate) doesn't really seem to me like an issue to be solved, as it carries its own risks and inefficiencies. This technique requires you to stockpile credits that could otherwise be benefiting your empire between market dumps. In addition, you're basically gambling that prices will go back up, which isn't guaranteed on the galactic market if an AI empire decides to sell off its own stockpile. Furthermore, artificially restricting resource flows to the market in order to inflate prices is a very real economic phenomenon (OPEC, anyone?), so I see it's existence in Stellaris as an argument in favor of the current model, not against it.
I also don't see anything wrong with the basic concept of having a 'baseline price.' It functions as a stand-in for the equilibrium price that would arise from the supply and demand generated by all the non-empire economic actors (individuals, companies, etc.) that exist in the universe of stellaris but aren't modeled by in-game mechanics. Implementing a system where movement of each individual good from empire to empire also strikes me as a bad idea, both because performance already struggles with the much-simpler system, and because Vicky II is proof that economic modeling and the sort of economic mechanics that make a game a game and not a budget simulator don't mesh well in the long term. I love Vicky II, but go play a Vicky II game past 1900 and tell me how much fun you had dealing with the late game economic crisis.