Both are Mini SUVs, We have Mini Pajero 96 model for almost 3 years, and Jimny 2009 660cc for 6 months now. Both suvs are good in terms of value of money. Second Generation Mini Pajero(1998 - 2012) is better than older models. When we compare these models we should compare New Mini Pajero(1998 up model) with current jimny model. Current Jimny appears around 1998 when Japan Regulation changed for Kei cars.
Some key points:
Mini Pajero production was closed in 2012 but Jimny is still in production.
Mini Pajero is more comfortable than Jimny as Jimny has rigid front suspension but still Jimny is lot better than Potohar(older Jimny)
Jimny is bit strong and better in off-road compare to Mini Pajero.
Parts are available for both cars in major cities.
Jimny is little bit expensive compare to Mini Pajero with same kind of specs.
I have 660cc Turbo charged Jimny with Automatic transmission. I often visit my village in Rawalakot on unmetalled roads. I never felt under-power also Mini Pajero 660 with Turbo. Jimny Wide( with 1300cc) is too expensive but not much different form 660cc turbo, Don't forget 660 Turbo engine power is close to 1200cc engine normal engine, don't confuse by these numbers. In Japan their is not much difference in their price.
Here are some compare links, in japanes, open in chrome with translated to English:
http://221616.com/car-topics/a_0000091878.html
http://autoc-one.jp/suzuki/jimny/special-365366/