They are both used but for different purpose.

Suigetsu is very useful to Azure Fangs for 9 tails, there is very few good damaging water ninjas and he is very fast to 5 star, so i maxed him just for that, however he is not good for your main team.

Tobi is probably the best easy to get ninja in the game at the moment and one of better ninjas all around even comparing him to rare ones, he is main team material for any main so if your main concern is your battle team then ignore Suigetsu and focus here first. Tobi/Hinata/GNW Kiba is very strong f2p water team for example.