Other M didn't have control issues. On the contrary, it pioneeered a new type of gameplay that has been years in the making.
You can claim they needed more buttons or using missiles with the motion controls was a bad move. But you can't really claim the game itself has bad controls when no other game has done what Other M did. I still contend the gameplay of the game itself was sound. They could have made a few tweaks here and there, but it wouldn't have changed much. And the 3DS wouldn't be able to 'improve' a game that was specifically made around a unique game engine and the WiiMote.
They just need to throw out the baby with the bath water and make a whole new Metroid with a whole new game engine. Because everyone seems to hate every single thing about Other M and won't accept what it actually did well.
Note: As usual I'm sure my views will be controversial because I don't hate every single aspect of Other M with a passion. For this reason, I'm probably not going to respond again in this thread to save people abouther 10 pages of 'Other M did everything wrong and anyone who disagrees is an idiot' thread.