Why are Metroid franchise sales so low? How can the franchise grow?

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That's actually a good question.

It looks like Metroid haven't been able to increase sales from the "first" game in both of the times the series has started.
It looks like the competition have always beat Metroid, or atleast eaten away its sales to an extent.
Kid Icarus propably got some of Metroids sales, both were adventure games (admittedly, Kid Icarus may have been more like a platformer), but KI was more linear and accessible.
By the time of Super Metroid, there was competition from Super Turrican (and on the Megadrive side, Mega Turrican), a game that have been compared to Metroid a numerous times (despite being a sidescrolling shooter and therefore more accessible). This argument is supported by the decline in sales in Japan, where the series declines in a same fashion with the sales of the consoles, while in the west, where Turrican is much more recognised, the sales drop is huge (especially in others, where SNES outsold NES).
After the series being on a break for one gen, it returned to GC as in the form of Prime. Metroid Prime did by far the best, if we look at sales on a relative userbase (2,7M on 60M installbase vs. 2,8M on 22M installbase). Prime didn't have any real competition on GC, until Echoes, which suffered from being compatible only with 60Hz TV:s and having Resident Evil 4 having its launch soon after Echoes.
Corruptions sales were most likely killed by RE4 Wii Edition and REUC, both being "the" games that Corruption was supposed to be, as how to control shooting with Wii Remote and setting standards to it. Also, it's worth noticing that Nintendo has noticed what is taking Metroid sales down, which is it having too much adventure elements, which can be seen by Corruption made as a more linear game than the previous installments in the series.

How to get the sales up, would propably require the series to turn into more action, less adventure, but if it can perform to level near 3 million in sales, i don't think there's really any need to make any dramatic changes into the series. But who knows, maybe they want the sales up to 5M level (although, if the Metroid Prime collection is coming out, it, then again, shows that Nintendo is willing to push the series "as is", among luring the "hardcore" for the console).