This is what you want, like, 99.9% of the time.
The 6502 just puts its address and data bus on pins, and you can make the memory map for your computer however you want, as long as you are willing to wire up the logic. There's no privilege for on-chip resources... everything is off-chip and completely equal. With the AVR, the resources (RAM, flash, peripherals) are completely fixed but much, much faster. There are a ton of chips you can buy with SPI / I2C interfaces if you want the AVR to do something interesting, and you drive them with the on-chip peripherals. The on-chip peripherals get to sit in memory somewhere, but the external ICs don't. With the 6502, you put things in memory somewhere, figure out a way to decode addresses on the bus, and use a parallel interface for everything.
A 6502 is a CPU in the "traditional sense". It has limited internal state in the form of a few registers, and communicates with the outside world with address lines and data lines; I only simplified a little there. Everything else is external: RAM, ROM, any external devices on a different bus (I2C etc.), even timers and GPIO need external circuitry with usually other ICs.
An AVR on the other hand tends to have all of that stuff (or at least a sizable subset) built in. That's, obviously, enormously convenient, and often means that with the AVR itself and just minimal external circuitry you have your needs covered. But it's less educational, you've rather plugged a computer into your circuit than built a computer.
Lots of us grew up with 6502 based machines.
Probably the main advantage of a 6502 is more RAM/EEPROM (as 8bit microcontrollers are pretty limited that way) and more of a hardware/software ecosystem to work with.