I made a couple cocktail tables similar to what you're making and i'd have to agree that if it's your only cabinet you definitely want the side by side joysticks in the front. If you're going to a classics only design, you'll probably be happier without it just for simplicity and lack of confusion when other people use your cab.
Question tho... Are you sure your front joysticks really need 4 way functionality? I'm hard pressed to think of a game that I play in a horizontal format that i've ever been frustrated with for lack of true 4-way joysticks. The cost of buying 49 way joysticks may not be worth it ($35 joy + $20 gpwiz + $13 cable + $10 gasket return + $? balltop + $15 ship all = ~$100 each). Let that extra money ride, and get yourself a nice spinner or trackball (or both!).
I actually do like the idea of 49 ways for the two ends, but still feel that functionally they are not enough to justify the cost. They have a round motion which most people feel is not ideal for most vertical games. Have you considered starting off with something with a restrictor plate (like a j-stick) and just cutting some slots in the bottom to twist the plate when necessary? I'm actually a big fan of the suzo inductives, but i know their short throw is an acquired taste. i acquired it when i saw my time pilot score double

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As far as the end joysticks go, in my case anyways, they are in 4 way mode 90% of the time. There are very few exceptions: gauntlet 4p, time pilot, time pilot 84, gaplus. I usually play with other people, so all my shmups play on the horizontal mode so that we can take on the forces of evil together. With the suzo, i just toggle a switch and i'm in 4p mode on both end joysticks

Also with the end joysticks, I think you would want to wire the end joysicks as controllers 3+4 instead of 1+2. I did this on my second cocktail. a couple reasons:
a. Some 4p games play rather well like that (gauntlet I + II), and some 3-4p games (Rampage, Off-Road, nearly any beat-em-up) play well enough that if you handicap yourself enough to keep the game interesting for your buds.
b. it's really quite easy to generate a couple extra controller schemes in your controller config file. any time you set a game to rotate the screen, just add the lines to the controller config for that individual game, and you're set. Some (like gauntlet) will require a complete rewrite of the directional controls for the character to move properly, and others that use relative controls (Offroad) won't.
c. Avoid confusion with people trying to play with the wrong controls. It's nice because with separate inputs they can't even start the game from the wrong controls.
that must be my longest post ever... good luck building your cabinet. adding a front panel makes for a lot more decisions, but also makes for a really versitile cabinet... I'm sure you'll find out what you want to do for controls, but i'd avoid committing myself to $350 worth of 49-way joysticks. Throw in the fact that Happ keeps on making the product worse, and it seems to even make less sense...