There are plenty of applications where Li-ion is not the optimal solution. Li-ion is not the defacto standard for a myriad of reasons in various sectors. Certain massive installations have requirements that li-ion cannot work for. For consumer electronics, maybe li-ion is the best thing we have but for other applications there are breakthroughs made on yearly basis.
Enerpoly for instance have prototyped Zinc-Manganese batteries that have great life-cycle, are rechargeable and have great power output for less than 40euro/KWh. In the next few years you will see more and more solutions targeting specific industries and needs. Li-ion is not a silver bullet as its production cost and lifetime is not the greatest of all the solutions offered.
http://enerpoly.com/technology/
Full Disclosure: I know the CEO of the company and this is not an ad or anything like that. I just want people to pay more attention to upcoming improvements in the sector.