I always, always use Shinji. If you like Shinji, use him, if you don't, don't worry about it.
You do not need to keep all your characters levelled, but you just want to keep in mind that you want at least one person who can heal multiple characters (though I would recommend having healing skills on your protagonist) and at least one other who can heal one person at a time in your party at all times -- this is pretty easy given that many characters in P3 have at least basic healing skills.
Just go with whatever party feels comfortable to you. I generally tend to use Akihiko, Yukari and Junpei (I'd use Mitsuru more, but she tries to charm enemies more often than I'd like), but a lot of people ditch Yukari for Ken later on or use Aigis instead of Junpei later on -- just depends on what you like. Akihiko is generally recommended since he is the most balanced character and he learns all of the de-buff spells which can come in handy during boss fights, especially if you find yourself a bit under-levelled.
As mentioned above, there's only one decision you need to make to go on the true ending path, and you'll know what it is -- your characters spend a lot of time agonizing over it.
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