This is not an unusual arrangement for EU airports. There are separate channels for arriving passengers, depending on whether the flight comes from a Schengen airport or not. Same for departing passengers. A large airport like FRA also has more than one immigration/emigration point for passport control.
A good decision.
Just for the record, a number of replies did not address the specific situation that you described: A single ticket with LH and/or partner airlines where arrival and departure at FRA airport are in Terminal 1 and, as far as I can tell, are even confined to the area of the A/Z gates. This blog entry probably describes various scenarios for transit / connecting times more accurately:
The following assumes both flights arrive and depart from Terminal 1. For those with through checked baggage or no luggage, on a single ticket, I would recommend a minimum 1.5 hour connection time, even though airlines can book you with a shorter connection time. If you're on separate tickets but with no luggage or through checked luggage, I'd recommend a 2 hour or more connection time. And if for some reason you need to collect baggage in Frankfurt and recheck it, I'd recommend … don't. More seriously, in that case, I'd recommend a minimum 3 hour or more connection.
And if you have to change terminals, say arriving in Terminal 2 from a Non-Schengen country and departing from Terminal 1, on separate tickets, I would add another 30-45 min. to the times above.