No doubt we all have slightly different ideas about what would make a good covenant. The real trick is to meld those ideas into a single functioning covenant.
As I see it, if we're going for a covenant in Thessiloniki, the absolute minimum boons/hooks are as follows:
-3 Urban: the covenant is located in a major city
-1 Road: the city is a harbor city with many people passing through it
Beyond that, it all seems up for debate. Here are some boons and hooks that might be of interest to us. I'm not saying we should take them all. But they seem the ones that might fit with a city covenant.
+3 Regio: the main portion of the covenant might exist in a regio in the city to which we control access
1+ Aura: the covenant might have a magic Aura greater than 3 (e.g., in one or more lacunae, or in a regio)
+1 Healthy Feature: Adauli suggested that the chapel might be considered a healthy feature
+1 Regio: the main portion of the covenant might exist in a ragio in the city to which we don't entirely control access
+1 Immunity: Adauli suggested that the chapel might grant immunity to certain common diseases
-1 Regio With Unexpected Entries: the main portion of the covenant might exist in a ragio in the city to which there is easy access by all
+0 Manor House: we could simply have the covenant made up of normal buildings, with one or two major buildings and a bunch of minor ones.
+0 Small Tower: we could have the center of the covenant be a tower, though this will be harder to explain since towers were mainly used for military purposes
+1 Edifice: we could have a particularly impressive building, though that might draw too much attention to us
+1 Secondary Income: if we're an old covenant, we might want a secondary income to keep our finances in the black
+1 Vis Grant: if we expect to have a lot of vis, we might want to give it away as a matter of right
+1 Wealth: similar to secondary income, we might want an added buffer for our finances
-1 Vis Salary: in the alternative, we could require the magi to perform services to the covenant to gain vis
+0 Peasants: the majority of our covenfolk could be normal commoners
+1 Literate Covenfolk: given that we're in the second largest city in the area, our covenfolk might be better educated
+1 Loyal Covenfolk: if we're an old covenant, we might have covenfolk who are a bit more loyal than green covenfolk
+1 Strong Community: if we're an old covenant, we might have covenfolk who are more tightly knit than green covenfolk
-3 School: Given that we're well educated and in a population center, we might potentially run a school (maybe even as a source of income)
-1 Guild: given that we're city-based, our covenfolk might be organized more like a guild (especilly if a source of income fits into a guild structure)
-1 Rights and Customs: if we're an old covenant, the covenfolk might have accumulated some rights and customs over the years
+3 Powerful Ally: given that the concept of this saga is coming out into the open, we might have drawn the attention and support of a powerful figure in the area
+1 Local Ally: similar to above, we might have only gotten the support of a minor city official or noble thus far
+1 Promised Favors: if we've agreed to help the local authorities (not sure where we are in that development), we might have some favors owed us
-3 Beholden: we might find ourselves under the thumb of the local authorities
-3 Mundane Politics: this seems an easy one, since the whole point of the saga is that we're getting more and more involved with the mundane world (possibly this might be a minor hook since we're saying that the local quaesitors aren't getting on our case for mundane involvement)
-1 Favors: instead of beholden, we might choose this to represent that we simply owe some favors to someone
-1 Hangout: given that we're in a major city, there could easily be an inn or a church were we hang out
-1 Rival: someone (hermetic or mundane) might object to us and work against us
-3 Meddlesome Saint: given the (still?) religious focus of our covenant, we might have come to the attention of a saint
-3 Seat of Power: we're right in the heart of the power of the current leaders of Thessaloniki (whoever those happen to be at the moment)
-1 Fallen Temple: we're in Greece; there's always the possibility of a fallen temple
-1 Festival: there might be relevant festivals (e.g. religious ones) that have an effect on the covenant
-1 Sanctuary: there might be a church nearby (on covenant grounds?) that can be used as a sanctuary
Then there's always the appeal of taking some mystery hooks to allow the SG to reveal something like diabolic corruption or a possession victim or spies or something equally interesting in the future.
Now, I realize that this is a very long list. I don't expect us to select everything on it. But I went through Covenants and looked for anything that I thought might possibly be relevant (I might have missed some). I thought this would be a good starting point for debate.