Honestly, you can mostly ignore the stories in the core SMT games. They can be summed up as "The World Ends" in 3 words, and it will be presented with few words more. There is like 2 lines of story dialogue every 5 hours of gameplay. I'm not overexagerating. So bury any worries you might have of diving into late into a big franchise like this and just play SMT3. The battle system is the most finely tuned in the entire JRPG genre. Also not overexagerating.
The spin-offs vary in quality, just playing SMT3 & 4 should keep you busy enough for a while, you can revisit the spin-offs later if you really want to.
I could not disagree more about smt plots being shallow. Just because they focus more on religion, the meaning of life etc over character interaction doesn't mean its less deep.
Mind you it does go into the crazy jrpg bullshit we all know and love but that's a given.