Well, for warmongers the science penalty is especially bad, because it triggers as soon as you take over the city, but the city won't actually do anything for you until it's out of rebellion. So, especially in late game, whenever you decide to go on that conquest spree, your science will basically freeze in place, and you'll only tech at a snail's pace. Earlier wars, when the population (and thus turns of resistance for newly captured cities) is lower, are not as bad, but teching then is arguably more important. So, it's lose-lose.
What each non-capital city needs to generate in science to be science-neutral in civ V (assuming it takes you 10 turns to get each tech):
Internet: 51
Telecommunications: 44
Ecology: 37
Penicillin: 30
Plastics: 24
Radio: 18
Electricity: 14
Scientific Theory: 9
Architecture: 7
Acoustics: 5
Medieval: 2
Classic/Ancient: 1
Pop in cities necessary to break even, with library, no specialists, no rationalism (as you can see, this is no longer realistic past industrial era):
Internet: 34
Telecommunications: 30
Ecology: 25
Penicillin: 20
Plastics: 16
Radio: 12
Electricity: 10
Scientific Theory: 6
Architecture: 5
Acoustics: 4
Medieval: 2
Classic/Ancient: 1
Pop in cities necessary to break even, with library, university, rationalism, no specialists (as you can see, at a certain point, you'd want to start working specialists; -2 pop required per other specialist, -4 pop required per scientist):
Internet: 21
Telecommunications: 18
Ecology: 15
Penicillin: 12
Plastics: 10
Radio: 7
Electricity: 6
Scientific Theory: 4
Architecture: 3
Acoustics: 2
Medieval: N/A
Classic/Ancient: N/A
Pop in cities necessary to break even, with library, university, schools, rationalism, no specialists (as you can see, this is where you want to be; -2 pop required per other specialist, -4 pop required per scientist):
Internet: 14
Telecommunications: 12
Ecology: 10
Penicillin: 8
Plastics: 6
Radio: 4
Electricity: 3
Scientific Theory: N/A
Architecture: N/A
Acoustics: N/A
Medieval: N/A
Classic/Ancient: N/A
If you're teching at a faster rate than 10 turns per tech, these requirements get upped.
If you're teching at a slower rate than 10 turns per tech, these requirements get lowered.
Overall, it's pretty rough on your science to expand. This is less of an issue for culture/diplo victories, where you only need one late game tech (and you can oxford or rationalism-finisher it). But, for science victories, going wide has its problems.