Nice idea for a game. It is not flawless, but still good.
While it mostly plays like a regular pinball game, there are some differences. First of all, you do not just die when Samus rolls off the board, you can also be killed by enemies. You have eight hit-points and you lose them when up against either Metroids or bosses. Another important difference, is that on a board you might activate a mission that requires you to stop at a certain spot, get out of morph ball and fire your gun. In addition there is a wall-jump mini-mission that you might also get into.
There are six boards, two of which are regular boards while three are boss fights and one I don't quite know what to call. On the regular boards you have several missions that you complete like defeat a wave of enemies or do the wall jump mini-game. Those two are available in the single mission mode from the start, while the other four must be unlocked through the multi mission.
In the multi-mission, you occasionally move from an area to another (you choose which one is the next). The regular boards and two of the bosses are available from the start, but to get to the special board you must collect all the artifacts (you get one for each mission) and then you must beat that level to get to the final boss. When you beat the final boss, the credit rolls, and then you continue the game. As with all pinball games, it all comes down to the score. You get some points while you play, and whenever you lose a life you get "bounty points" for the enemies you have killed so far. There is also a multiplier for the bounty points which can be increased up to 10.
The controls are simple. You use L or left on the D-pad to use left flipper and R, right on the D-pad or A to use the right flipper. When Samus stand and fire, she fires automatically and you rotate her with the same buttons. You can also require missiles, which are set to X and power bomb for Y. Sometimes you get into a scanner that decides a bonus for you, then you have to press B to make it stop spinning.
While Metroid Prime Pinball is an original idea, taking out enemies can sometimes be really bothersome. Some of the enemies will be on the lower screen, very close to the flippers, so if you are unlucky, you might hit it and then the ball goes straight into the gap between the flippers. That is one out of several flaw which will bother you more or less. As far as physics go, I don't like the game quite as much as 3D pinball space cadet (which you may have played on Windows XP), and sometimes the game just makes me think about how great that game was. It is a bit too hard to use the left flipper to shoot the ball towards the left, and at some points, shooting the ball in the right direction is really crucial, which makes it annoying when it ends up on the wrong side.
I have one big issue with the final boss fight: In any boss fight, the boss itself ought to be tougher than regular enemies. Instead, I find the Metroid that turns up to complicate the boss fight more challenging than the boss itself. The thing about the Metroids is that when the ball comes down from the upper screen to the lower slowly (which it often will) they can catch it and take two hit points (as mentioned, out of eight) before they drop it again. Therefore you really need to take out the Metroid, which since it is on the lower screen leads to the problem I have already addressed.
Another problem that bothers me with this and many other pinball games is that the gap between the flippers is a bit big, so if the ball comes down at an unfortunate angle, there is really nothing you can do to prevent it from being lost unless you are fortunate enough to have the force field turned on at that moment (a beam of life that connects the two flippers so that the ball can not go down between them - lasts for 30 seconds).
In the end, Metroid Prime Pinball is a fun game, but occasionally it might feel like luck plays a too large role in it. It is a game that has a lot of replay value if you fall in love with it, but if not it is really short. To increase the experience it has multiplayer, and if you have a DS that is not the DSi, then it adds to the experience that there is a rumble pack which you can insert in the GBA slot. MPP is not a bad choice for a game to play on the go.