First off, bear in mind the RM series are built for fast and easy building of "CLASSIC TURN BASED RPG", anything not in that category are ditched and not added to the game maker UI by default to avoid the confusion and distraction of beginner game developers. If you want something not provided by default, you will need to add scripts to add those features and control them via scripts alone.
Why not use GG Maker where what you want is already a built-in feature?
GG Maker isn't restricted to building rpg alone, you can make tower defence, shooting, platformer, racing, action rpg, etc etc, imagination's the limit.
http://www.rpgmakerweb.com/products/programs/gg-maker
You can build the HUDs and Layout of your Menus and Interface however you like there using the wysiwyg graphical tool.
It's just a small comparison in between the advantages and disadvantages.
RM series is still a great tool for beginners, BECAUSE of the restrictions.
There's a lot you can't do but you get to make the easiest and simplest RPG game in the shortest way available, without other unwanted functions to confuse you.
But when you don't want what RM offers by default, they lost their value overall when it comes to freedom in creativity. You can only create turn based rpg by default. The rest require 3rd party script support.
The best things RM series ever offered are: (If you don't find these 3 interesting, you will be more happy starting off with another game maker)
[1] Turn based battle system that is offen used in the classic rpgs. (you won't find a better written turn based system out there)
[2] Level curve editor/calculator for exp and stats (yes, it's possible to build one ourselves, but the time needed for that good balancing is crazy)
[3]
RTP, a shared contents concept that allow creators to build games using the smallest download size available. (The main reason why RM is being loved by the doujin circles)
And sadly, that's all of the advantages i can think of for RM series, the rest of the functions they provided can be found in almost all of the game maker softwares out there.
What RM series lack compared to other game makers out there:
[1] This software is build in mind to create a turn based rpg game in the simplest way. Ditching all other possibilities that aren't required by a turn based rpg game, keeping everything to the simplest. (Great for beginners making their 1st rpg, but when you want more, you will hit the restriction wall)
[2] The freedom in creating game scene (UI/layouts/HUDs)
[3] The freedom in controlling the game mechanism (aka, scripts. while other game makers provide wysiwyg chart wizards)
[4] Restricted layouts and game structure. You can't change or add anything without external scripts. You will have trouble trying to build non-rpg games due to some built-in codes.
[5] RM series before RMMV do not support GPU, making process resource and power limited and can easily lag with a bad script or just tons of events on screen.
So when someone come by saying, i don't want the built in turn based battle, i don't like how the levelling and stats works, i don't like the menu layout and want to design my own, i don't want the provided default graphic. Then yes, it's time to tell them they bought the wrong software.