http://revach.net/article.php?id=3762

Section: Halacha   Category: Tefila
She'arim Metzuyanim B'Halacha: Which Shul Should You Daven In?
The Kitzur Shulchan Aruch (12:9) brings that if there are two Shuls in your city, you should go to the further one since you have Schar Pesios, a reward for each step you take.  The She'arim Metzuyanim B'Halacha says this is based on a Mogen Avrohom (90:22).

However he brings from the Sidur Bais Oveid that this only applies to women not to men as the Mekor in the gemara Soteh (22a) that talks about Schar Pesios refers to a women.  The difference being that a women is not required to daven in Shul.  Since a man must daven in shul, if he may not pass by one shul to go to a further one because Ein Ma'avirim Al HaMitzvos, we don't skip over mitzvos.   

However ays the She'arim Metzuyanim B'Halacha this rule only applies if there is no legitimate reason to skip over the mitzva.  In that case it is an insult to the mitzva.  But if you have a reason to daven at the other shul then this Klal does not apply and you may daven in the shul where you feel more comfortable and you will daven better.

Important Note: We try to convey the Tshuva to the best of our ability. We admit that our understanding may not be accurate. One should learn the tshuva to verify the accuracy of our interpretation.  Please also understand that this Tshuva may not be the final word on this topic. One should consult a Rav before drawing any conclusions.