Why do microcontrollers have so many functionalities at once?
Those peripherals are necessary for most real-world applications of microcontrollers, Not all of them, but leaving out any subset would decrease the market for the microcontroller. For example, the Scenix microcontroller family which was very fast but had very limited hard peripherals was a resounding market failure. That's really bad news for those of us charged with specifying microcontrollers- a complete redesign in order just to keep your products going (okay, maybe good news if you're brought in to replace the person who specified the oddball micro and subsequently paid to clean up someone the mess they left, but that's not great fun either). Much of the area on the chip is taken up by the memory and the bonding pad/drivers and the CPU so those little hardware peripherals are pretty minor. 

If you need more processing power, leave the world of 8-bit micros behind and move to one of the 32-bit ARM cores which are generally used in microcontroller-like situations but have more of the chip area devoted to the processor and often to the memory. Or a DSP or FPGA can offer orders of magnitude more processing power, suitable for video processing, high end audio, high end instrumentation and data acquisition etc. As it is, the processing power of modern 8/16 bit micros is not all that bad, and often we 'waste' it by using a high-level language to gain other advantages (faster development and prototyping, use of commercially available libraries such as protocol stacks) rather than tediously hand-crafting bespoke code in assembly.