Are there any disadvantages in high pin count MCU?
There are some disadvantages (and some advantages) depending on application.

For a well defined project that will not be changed (things do change quite often) then having the smallest package that will do the task is often advantageous.

Specific disadvantages:

1 Power consumption. The larger packages almost universally have far more internal circuitry which can use power, although with the latest MCUs, this has been overcome to a great extent by being able to stop the clocks and sometimes power down unused features. See the EFM32 series for parts that can do this (there are many other series parts that have the capability - this just happens to be a series I am familiar with).

2 Code and documentation complexity. With all those added features, if you do not intend to use them, then you need to ensure those features are indeed off (they are often disabled by default but you will need to check all the same); in addition, a modern microcontroller reference manual (which is where the real meat of operational details are usually documented now) often runs to several thousand pages which you will need to read and understand even for features you do not intend to use to ensure you have no unwanted side effects. The amount of documentation is proportional to the number of features available.

3 Errata. The more complex the core and peripheral set (and as we increase pin count for MCUs, the more complex they typically are) the greater the chance of something being not quite right. This is the subject of the errata (which I have seen span more pages than the datasheet on many occasions and can be different on a batch / date code basis). Errata may or may not actually ever get fixed with silicon updates so you have to use the available workarounds (if available) in those cases.

4 Solderability. The higher the pin count, the higher the chance of a poor solder joint. For a xQFP type package, coplanarity (which defines how well the pins are aligned for PCB mating) is a key issue and if the device has been mishandled there may well be pins (that you may or may not care about) not being soldered. Note that every pin should be soldered for mechanical strength even if the pin in question is not actually going to be used in your application. Higher pin counts can increase the cost of the base PCB.

There are MCU families that have the same core with differing pin counts and consequently expose fewer features on the lower pin count parts.