I don't think it's really a neglected series (other than the N64/GBC where we saw nothing of it outside of Smash Bros) but it's easily among the 'big names' that Nintendo has that doesn't get as much love as it deserves.
I mean, we see Mario and Donkey Kong literally all the time, whether it's in their own platformers or in some multiplayer game, we see them waaaaay too much. The Legend of Zelda is not far behind with 4 Zelda titles released so far on this gen of consoles, 1 incoming and a few obvious cameo's in other games. We'll not talk about Pokemon...Animal Crossing and Fire Emblem are quickly becoming their new franchise to milk.
To be honest, if we didn't see so much of their other characters like Mario and Link plastered over almost everything, Metroid probably wouldn't seem as few and far between as we view it. Hell, just throw Samus and Captain Falcon into a few more games as a playable character and we'll be happy that we've at least seen the character regularly...Which is why I think 'Mario does thing' games should be rebranded as 'Nintendo All-Stars' so that we can see some more damn variety.
nintendo franchises can be divided into 3 tiers. the top tier is mario, zelda, and pokemon; franchises that even if youve never played a game in your life odds are you've still heard of these. metroid (along with kirby, star fox, and animal crossing to name a few) are mid tier; franchises known and loved in the gaming community but not the general populace as a whole. finally theres the low tier franchises (examples of pikmin, fire emblem, and earthbound); franchises only big nintendo fans will recognize and likely the only ones who will give the game a chance.
i understand there are people who really love this franchise and want to see more of it, and theres nothing wrong with that, but some people act like because the franchise doesnt get a game every single year that nintendo has somehow "given up" on the franchise or are "turning their backs on fans" when they really havent. like i said earlier its been 5 years since the last metroid game, but you know else has had a 5 year gap? links awakening and ocarina of time (1993-1998) and you know what else? elder scrolls oblivion to skyrim (2006-2011) and you know what else? city folk to new leaf (2008-2013 for america and europe) and you know what ELSE? xenoblade (for japan anyway) and xenoblade x (2010-2015) the point im trying to make is 5 years really isnt all that long in terms of gaming. heck metroid has had a longer drought of 8 years from super metroid to prime/fusion (1994-2002), there was a 9 year gap from pikmin 2 to pikmin 3 (2004-2013), 15 years from super punch out to punchout wii (1994-2009) and TWENTY-ONE years from kid icarus of myth and monsters to kid icarus uprising (1991-2012).
the reason you see mario link and pikachu everywhere in nintendo is cause they're the biggest sellers, and at the end of the day, the cold hard truth is nintendo is a business and the end goal is to make money. yes it would be nice to see more metroid or whatever other franchise one feels doesnt get enough attention, but unfortunately some of these franchises just dont sell well enough to justify releases as often as mario or zelda. and we DO see references to other franchises in certain games (like in smash bros and certain furniture or outfits in animal crossing and now mario kart with excitebike and f-zero courses), just not as often as some people would want. its when they STOP referencing it that you should panic about the franchise, but if color tv games can be referenced in smash bros 37 years after the fact (the first color tv game came out in 1977) nothing is impossible at this point.
i honestly believe one is in the works, its just not ready to be shown yet, which is something else people need to consider; nintendo wont show something until they feel its ready to be shown. they dont want to pull a "duke nukem forever" or "last guardian" where they show off the game, and then give the extremely tentative release date of "when its done," cause after awhile people would just give up on the game ever happening.
so to end this off, dont give up hope for a new metroid or whatever franchise you want to see more of, but also acknowledge the reasons behind why it doesnt show up as often as mario or zelda and realize nintendo is doing their best to give people what they want, but at the end of the day, money trumps everything else for better or worse.
TL;DR 5 year gap doesnt mean its gone forever and if you really want to show nintendo the games you want (or dont want), vote with your wallet.