Can I use "put two and two together" in this case?
Here's the scenario:
I'm moving next month. The new place is actually farther away from work, but is much bigger. Besides, the rent is the same and everything there is new. By farther, the subway ride to work is ten minutes longer but the distance between my new place and the subway station is five minutes shorter. After "putting two and two together", I think it's worth moving there.

If not appropriate, how can I rephrase it to mean "after taking everything into consideration" without sounding too formal?

Question

Can I use "put two and two together" in this case?
Here's the scenario: 
I'm moving next month. The new place is actually farther away from work, but is much bigger. Besides, the rent is the same and everything there is new. By farther, the subway ride to work is ten minutes longer but the distance between my new place and the subway station is five minutes shorter. After "putting two and two together", I think it's worth moving there.

If not appropriate, how can I rephrase it to mean "after taking everything into consideration" without sounding too formal?

Answer

You said it best by saying, "after taking everything into consideration."

You can also use "All in all," or "Everything considered," or "When all is said and done,".

"Putting two and two together" is used when certain actions begin to arouse suspicions:

"Without those glasses, Clark Kent looks a lot like Superman, and he is never there when Superman is around. Why can't Lois Lane put two and two together?"