Some suggestions?

Can anybody tell me a good microcontroller, whether attiny or mega, that has native USB support like the Atmega32u4? I want one that isn't smd, but a dip. I want to build my own arduino clone.

Pick your favourite!
Atmel AVR device selector

hansibull - that doesn't have a feature to filter by package.

But don't bother, I've looked, Atmel does not manufacture any such AVR micros in DIP package, and I've honestly never seen one from other vendors either.... Only native USB AVR supported by arduino is 32u4

All the best (in some areas, all the good) parts are SMD only nowadays - you're just going to have to learn to work with SMDs.

The whole board is a DIP:

Knock-offs from Aliexpress are going for about $3.40 USD shipping included. So, you're not going to buy the MCU, USB connector, crystal, resistors, and capacitors for that little.

But, if you really want to get into "from scratch" anyway, check out what john1993 shows in this post, I think it is very interesting:
https://forum.arduino.cc/index.php?topic=390148.30

There are no AVRs in DIP that have USB.
There are some Microchip PIC32 devices that might work, and might be supported by Arduino-like IDEs.
There are some other Microchip devices in DIP with USB, but not very Arduino-compatible.
Very few DIP uCs with USB from other vendors :frowning: