Leading questions:
Representative vs Direct Democracy?
Unitary or Federal?
Presidential or Parliamentary?
How much separations of powers should there be? In presidential systems, such as the United States of America, there is often deadlock between the executive and legislature. In parliamentary systems, the head of government is elected by legislature, therefore, there is practically no deadlock as long as theres is majority support of the executive in the legislature (although, there can still be courts to determine constitutionality of policiss). Would you prefer more checks and balances, but can also result in more deadlock, or a government more easily able to enact policies, for better or for worse?
Electoral method? FPTP? Two-Round? Ranked-Choice/Single-Transferable Vote? What about legislature? Should there be local districts? Single or Multi member districts? Proportional-representation based on votes for a party? If so, how should the party-lists be determined?
Should anti-democratic parties be banned? Or should all parties be allowed to compete in elections, regardless of ideology? In Germany, they practice what's called "Defensive Democracy" which bans any political parties (and their successors) that are anti-democratic. Some of banned political parties include the nazi party.
How easy or difficult should the constitution br allowed to be changed? Majority support or some type of supermajority support?
Should we really elect officials, or randomly select them via sortition?
These are just some topics to think about, you don't have to answer all of them.
Edit: Clarified some things
I think your first point is just a reality for any representative model. The best this model does is introduce more direct accountability at each level.
To your second point, I suggest drafts that trickle down, and votes that trickle up. I'd recommend formal proposals to be voted on for most issues, and transparent records to review at subsequent meetings for the rest. Representatives should be largely a formality when it comes to voting, like EC electors. Their main independent function would be debating issues and summarizing those debates for their constituents.
As to your third point, it's an interesting consideration. On the one hand, I would suggest a special election for the lower district to replace them. Perhaps even make the runner up a vice-representative to help conduct meetings and seamlessly step in in the case of the reps election to a higher district. On the other hand, I like the idea of even the highest representative maintaining some connection with every level of democracy, to keep them grounded. Certainly higher offices would require more clerical staff. I will give it some consideration.