Call lightning only works if you have an area with a 60' radius, 10' high space for the clouds to appear. So in a large amount of the dungeons in "Dungeons and Dragons", it doesn't work AT ALL. Not being able to use it in houses, caves, dungeons, castles, and so on is a huge, huge limitation. Big points to moonbeam. Moonbeam can be cast at level 2 for 2d10 damage, and does the same damage as call lightning at higher levels. Point to moonbeam for letting you 'downcast' by a level. Moonbeam appears in a place and does damage, you only need to spend actions if you want to move it. Call lighting only does damage if you spend your action. Point to moonbeam. Moonbeam can be moved 60' per round, call lightning can only happen in the original 60' circle. Point to moonbeam, but either of those is unlikely to be a limitation in practice.
Moonbeam does radiant damage while call lightning does electrical, not much difference. Moonbeam uses con save while call lightning uses dex, I'll call that even since there are more good con saves than dex saves but some dex saves get evasion. Both have the same 5' AOE, no points. Moonbeam has the 'unshifts shapeshifters' rider, but that's so situational I won't call it a point. If you're outdoors in a thunderstorm, call lightning has an effectively unlimited area and gets an extra d10 damage. This is so situational I won't call a point for it, but did mention it to forestall someone 'catching' it.
I consider moonbeam a solid default spell choice, while I'll only take Call Lightning if I expect to be fighting outdoors in a thunderstorm, and even then that's more flavor than anything else.