Now, every motor is different, and I don't know the ins/outs of the 2.5L... is it known for being air rescted in stock form?
As a general rule, a running engine is a balanced system. Basically a big lous air pump. You can only suck in as much air as you can push back out... short of forced induction, the amount sucked in is in fact controlled by the exhaust rate. As a result, increased intake will only have really noticeable benefit if you likewise open the exhaust (headers, wider exhaust, etc etc).
Just a thought.
On the cone filters, while they get dirty on the outside, the threat of sucking water/mud through is actually pretty unlikely. You'd have to have 100% of the filter submersed before that'd happen, short of what can just naturally pass through the filter with minimal pull.