Peach's Castle Live Show (kids need a live show, with comedy skits and stuff)
Warp Paper Water Park
Mario Circuit (Go Karting is a must!)
Yoshi's Island (for kids, with yoshicopter rides and teacups and stuff)
DK Minecart Coaster (especially if they can put a jump in, mwahahaha).
Luigi's Mansion
Warioware Arcade (classic and modern Nintendo Arcade machines are a must; from Sherriff to Pokkén and anything else)
Link's Crossbow Training Temple Ride
Wind Waker Flume (King of Red Lions instead of a log)
Lon Lon Ranch BBQ and Milk Bar (Who doesn't want Smokey Dodongo Ribs?)
Metroid 3D experience
Starfox Assault Coaster (just re-purpose the Hulk ride, it already suits pretty well)
F-Zero Coaster (use some of the bullet train tech for magnetic rails and ludicrous speeds)
Pokémon Petting Zoo or Safari Park (not actual pokemon, obviously, but the inspirations of)
Dreamland Cafe (including themed play area and ball pit of course... preferably all ages, but I understand if not)
Hot Air Balloon Trips
Wii Sports Bowling and Mini-Golf
Crossing Town (can include nintendo museums in the houses and a bunch of merch shops)
Pikmin Gardens (and a themed crepe or ice cream stall of course)
Steel Diver Sub Pond (like a battle boat pond, but with steel diver subs instead)
Ice Climbers Indoor Skiing
Fire Emblem Battle Show
Earthbound Diner
Splatoon Paintballing
Art Academy Gallery (Where they show actual fans art perhaps?)
I can't think of anything good for Kid Icarus... I guess just another coaster, but there's three already... Maybe the 3D Expeience if they have another Metroid thing... say Laser Quest? I dunno, KI's flying could work pretty well, but so could metroid...
As for the Dr Doom Drop... Maybe Pilot Wings?
Sadly there's not enough space in the Universal park for all of this, but there's some ideas.