Granting all priests an equal number of spells is not the same thing as having the same power level. It doesn't break verisimilitude in the least, because lesser deities have smaller churches, fewer worshipers, more narrow portfolios, and smaller divine domains.
Let's do the math.
Greater deity A has divine power X (coming from his 10,000,000 lay worshipers), which he can divide among his three avatars, five Chosen, twenty proxies, and 10,000 clerics (one cleric per 1,000 worshipers seems reasonable).
Let intermediate deity B have roughly one third of deity A's divine power because he has only about 3,000,000 lay worshipers. But he only has one active avatar, one Chosen, three proxies, and only about 3,000 clerics.
Not only can deity B grant his clerics the same level of power as deity A, but he has power to spare because he has fewer Chosen and proxies than his power level currently allows.
If you want verisimilitude, make sure that churches of weaker deities have fewer power centers, less cash, and less influence than churches of more powerful deities. Limiting clerics' spells is really poor design (and doesn't make sense, as I showed above).
Sammael, you made assumptions to prove your point. If the assumptions don't hold the proof doesn't either.
For example, you assumed above that the power of a deity is directly proportional to the number of worshipers. Maybe it goes as the square. or is exponential.
Maybe a greater god is known and worshiped on a hundred worlds, or a thousand, while a lesser god only has followers on 10 worlds - or just one.
Perhaps, just as a spell caster must be level n to cast mth level spells, a god must have a certain rank to grant spells of a certain level to clerical followers. After all, granting spells of any level to followers across the world (or the multiverse) is beyond the power of any mortal, so the argument that "gods are so much mightier than mortals" doesn't hold water either.