I haven’t extensively tried or used Citymapper (I just downloaded it to compare now), so this is going to just be initial impressions:

I’d say I prefer Transit just because it shows how far the bus is down the line from you, while that info doesn’t seem to be shown on Citymapper. I also don’t like that Citymapper doesn’t make the subway line names reflect the local transit line colors (ex: A line is blue, B line is red, etc) the way Transit will.

I do like that Citymapper has the subway map built in, but my city also has a bus map available that they didn’t include.

That said this is probably completely regional, go for whichever one works best for you.