2012 Japan Elections voided due to malapportionment.

[Okay, maybe Mike Johnson is a competent parliamentarian.]

Not the whole elections, just elections in a couple of districts in Hiroshima. Interesting that the courts in Japan are actually getting serious about the problems of malapportionment, though.

What are Japan's issues with malapportionment?

Severe. The 2009 election had constitutional issues as well. Places like Shimane and Tottori have notably more per capita representation than places like Tōkyō and Aichi (like with some single-district states in the US, but considerably more drastic, as you can see with the proportion that krazen quoted, which I think is a comparison of either Shimane and Chiba or Kōchi and Chiba), and I'm pretty sure the size of constituencies within prefectures varies widely as well. This is in part because Japan has no defined redistribution process, instead doing full or partial redistributions ad hoc on a schedule of approximately 'whenever the Diet feels like it'.

[Okay, maybe Mike Johnson is a competent parliamentarian.]

Yeah, the urban-rural divide in Japan is weaker than in a lot of other countries, although it's true that a lot of rural prefectures have or had big LDP machines. Parts of urban Kanto and Kansai are obscenely right-wing (like, considerably further right than the LDP mainstream even under Abe) and a lot of the remote north is by Japanese standards fairly left-leaning.

[Okay, maybe Mike Johnson is a competent parliamentarian.]

the LDP is increasingly a party of rural conservatism and not the flashy urban conservatism of the JRP.

So much of the tragedy of contemporary Japanese politics is wrapped up in this statement. The differences between rural and urban conservatism (and inaka and tokai in general), the pathetic problems with the former, the terrifying problems with the latter, the unfortunate ascendancy of the latter, the dominance of both over the political and ideological spectrum as a whole...

[Okay, maybe Mike Johnson is a competent parliamentarian.]

the LDP is increasingly a party of rural conservatism and not the flashy urban conservatism of the JRP.

So much of the tragedy of contemporary Japanese politics is wrapped up in this statement. The differences between rural and urban conservatism (and inaka and tokai in general), the pathetic problems with the former, the terrifying problems with the latter, the unfortunate ascendancy of the latter, the dominance of both over the political and ideological spectrum as a whole...

Please elaborate; I'm not familiar with the differences.

The shortest possible answer is that urban Japanese rightism is considerably shriller, flashier, less attuned to the concept of compromise, and, frankly, these days a form of palingenetic ultranationalism--one need only look at the name of Governor Misogyny and the Hashists' political party to see some evidence of this. The problems with rural Japanese conservatism are, as best as I understand them, more or less special cases of the problems of Japanese ruralities as a whole. It's traditionalist, often machine-based, and increasingly unable to defend itself from rigorous intellectual, political, or social challenges.

[Okay, maybe Mike Johnson is a competent parliamentarian.]

Someone should strike down the US Senate because of malapportionment.

I could theoretically see a SCOTUS with like 7 liberal appointees ruling that Senate apportionment without respect to state population violates the 14th and 15th Amendments.  The remedy would probably be to give the large states a bunch of extra Senators, not to abolish the chamber entirely.

Except the Constitution explicitly says that not only is the Senate defined as representing each state equally, it's (according to dominant interpretation) impossible to change that even through amendment without the consent of every state involved. It's the one single solitary entrenched clause in the Constitution, and the Constitution can't be held in violation of itself.