I apologize if this has been discussed. I went back two pages and couldn't find a thread on it. 

With the traditional DS, there are many games that utilize the touch screen and/or dual screens in unique ways. With the way the 3DS is designed, it would appear to be, some of these great ideas will go on to die. I'll use examples of DS games to show what we may lose. Here's what we know about the 3DS that is relevant to this discussion:

1. The screens are two different sizes. 

2. The top screen is 3D, but not a touch screen.

3. The bottom screen is a touch screen, but not in 3D.

So let's delve in the first obstacle, games that utilize both screens in play. The main examples are Contra 4 and Yoshi's Island 2. There are two problems with this format now, one of which is minor and one of which is major. A minor problem is that the screens are two different sizes, meaning either the top screen will support more action or they'll black border the top screen to make it the same size as the bottom. Secondly, only one screen has 3D, so when the action hops to the bottom screen, we get traditional 2D action. Looking at one 2D and one 3D screen to get a full picture of action as in a game like Contra could be too disorienting. My verdict is that this form of game is dead on the 3DS.

The second obstacle are games that you directly control a majority of the action via touch screen. There are numerous titles that do so, but I'll break it down into specific types of games to show how many can be affected. Note that because we should assume the action will be presented on the 3D screen, that means we lose the ability to manipulate our on screen characters directly.

Single character controlled Action-Adventures (and other genres) where you move your character, strike, and pull up menus via the touchscreen(Zelda, Chocobo Tales, Dragon Ball, The World Ends With You, Ninja Gaiden)

Turn-based Strategy games where you have the option to use the touchscreen to control movement, menu options, etc. (Disgaea, Advance Wars)

Puzzle games that you manipulate directly with the touch screen(Meteos, Peggle, Picross, Professor Layton)

Rhythm games where you use the touch screen for on screen action (Elite Beat Agents, Jam Sessions, Rhythm Heaven)

Other Misc. titles that use the touchscreen to directly manipulate the on screen action (Nintendogs, WarioWare, Viva Pinata, Anno/Dawn of Discovery, Korg DS-10, Phoenix Wright, Trauma Center, and many, many more titles)

I understand that with a accelerometer, gyroscope and 3D screen we'll be awarded with new experiences. However, are we giving up great past experiences on the DS in favor of this? How will developers attempt to see their way around this?

Are you assuming that every game with use 3D?

Ehm, you are totally right on most of them but I don't understand why you would not be able to play FPS or flight games any more. I also am very curious how the new professor layton will work, especially when they talk about 3D puzzles because you can't directly manipulate them.

You know that ds games are not using 3d. They are not made for 3d some when you play them they will be 2d. And the screen thing. I am pretty sure they are going to do the same thing they did with gba games on the original ds. They are going to same 4:3. So the image on the top screen will have boarders. So the obstacles are now cleared. Get hyped for this now.

Yes I am. Unless something has been officially presented differently, I expect based on it's namesake that every game will utilize the 3D feature, just like when Nintendo named the original the "DS" every game used both screens to some capacity. However, that is an awful lot of series that would have to lose their claim to 3D if they plan on controlling the same way as they previously did.

I'm not talking about playing DS games on this device. I'm talking about the future of these and many other 3DS games. How will the 3DS games of these and similar series control now if they can't replicate the old control scheme and 3D simultaneously? Do we revert back to antiquated analog gameplay, after the DS broke so many control barriers?

You're right. I forgot that the FPS games use the bottom screen to control and the top screen as the action.  I thought for a moment you controlled the action directly on the same screen. I assume you mean the same with flight games, but I can't find my copy of Star Fox to check. I'll remove both from the list. 

Well, Contras 4 will continue to exist... they'll just use 3D on select parts - like in those 3D levels. No biggie.

It's not like the whole game has to be 3D, just like most games now don't use touch screen all the time, but on a few select times.

you can turn off the 3d, so no problem exists, plus the entirety of the top screen doesn't have to be used

Turn of 3d, use DS controls, where is the problem, the 3DS has the same controls as the DS, plus extra stuff, so if you don't want the extra stuff, just don't use it