My advice : Stay away from arduino and API like arduino.
1) They are overpriced. Today, you can get development board for many mcu brand, including some atmega, for around 10$. Getting an arduino at such price is an impossible task, at least, if you want a legit mcu. I don't recommend buying non legit chip, it may just waste your time debugging some "extra non intended feature", not present in the official chip, also know as bug. Those chip are maybe not false mcu, but maybe just either stolen, or one that failed some test and got saved from garbage from some aliexpress seller. Save yourself the effort of debugging non legit chip. Of course, you may get some legit arduino at nice price in some event, like last year arduino day from sparkfun.
2) Lack of debugging : In the official arduino, the only mean of debugging you got is printing over serial. But what happen if the bug has to do with serial? Or the debugging over serial break the realtime of the project? print take lot of processor time. Also, if you intend to really learn embedded system and work your way trough register, how may you debug setting up the frequency and uart with print debugging without being able to print?
3) Using API such as arduino + wanting to get your way at register level = large risk to break some arduino API related stuff. You never know, by setting up pwm or timer or changing frequency which part of the API you may break. For example, by re configuring timer, you may break the delay function(incorrect delay value). And unfortunately, which feature you may break by changing which peripheral is not the most documented thing. So by wanting to do thing progressively by mixing arduino stuff + your own register level (aka the real way stuff) may be more error prone than going the full register way.
4) Programming on arduino teach some bad programming habbit. Multitasking with delay, no interrupt (except by going to register level and by forcing some handler, see point 3, MAYBE breaking up some API), is not a good thing. What you really need is going sleep + interrupt + state machine. When mcu doing nothing, no delay, but sleep. Some interrupt watch out for some event and guide out the state machine. Another way is to go RTOS, or to mix up RTOS + state machine in each process/thread.
My recommendation, go with a developpment board priced around 10-20$, from a legit source, with either onboard debugger or a porribility to plug your own debugger. (Altought you may plug a jtag to arduino, it require some modification to the board, and debugging the debugger -> mcu interface... no thanks). But yeah, arduino is a good idea. When you design, try to make thing as modular as possible, to make reusable code. Take example on the arduino API, and adapt it to your programming.
Some possible board: Any ST discovery/nucleo board, any launchpad from TI (in TIVA or msp430/msp432, don't touch hercule or c2000, too much advanced/specialized stuff), Freedom board from Freescale, some atmel xplained board (i think its the name), those nice psoc board... Almost every mcu has some affordable board. Just think about which path in the long way you want to follow.
Doing low power stuff? msp430/msp432, stm32l0/stm32l1/stm32l4, some kinetis, ANY silicon labs mcu
Want to get in the big train and get mainstream as much as possible? : arm cortex m0/m3/m4, as your power need rise.
Want to get lot of connectivity? Maybe you like IoT project? arm cortex or pic32 got many connectivity
Your personal project is geared toward DSP or radio frequency? Why not some cortex m3/m4 or pic23/dspic
You are more an hardware guy and thinking with the practical side of the project and don't want to focus too much on the programming aspect? Why not cut off your development time and go with some 8 bit mcu? AVR is the easiest one, very clear datasheet. Except if you need CAN or some other functionality, don't go with pic18. Pic18 is overpriced performance wise. AVR also, but at least you get a nice architecture. But if your programming need is simple enough and just want some more advanced peripheral, why not go with pic16? Not as overpriced as pic18, and include the most recent peripheral from microchip, including hardware PID controller... YEP, a full PID where you just set up 2-4 register, and no software overhead.
Just try to figure out the main area of focus of you future personal project, and we may help you selecting the perfect mcu for your need.