Interesting question, in Australia early Gallardo have gone up in value about 15%. I suspect there is still depreciation in the latter cars as the type1 buyer (Latest and greatest )updates. And Hurican are the flavour of the week.
History tells me that 04 manuals will be popular choice. A couple and some will say odd reasons, they don't have nose lift,
Koni shocks, oddly the ultra close gearbox, plus they were the first of the new era.
That is strictly your opinion. Usually people who buy first gen are due to cost. I and most people did it because of cost. I assure you it is not just my opinion.
If you really want a gen 1, the 06~08 are far superior choice in terms of fun factor on the road or on the track to 99.9% of people except you and for the small price difference 06 offers everything 04 is and so much more. 04 Manual might have a chance to be considered collectible car someday due to the limited quantity and limited choices of newer manual cars from other brands. The appetite for manual car is huge with so few cars to go around.
History tells you the improved version of any particular model will be popular choice if cost is not a big concern. Take 2009~2011 CBA GTR for example (I had one too) vs 2012 DBA GTR. When people shop for a GTR only reason to go CBA is also cost. DBA offers so much more and their market value reflects that.
Another example is 360 VS F430. The only debate for 360 is if people prefer the look, it does have one sexy rear end. But it is so far inferior mechanically and performance than F430 (I had a manual 360 too). The old NSX 91~96 NA1, 97~01 NA2, 02~05 NA2. The 02+ worth at least double of the NA1 (I too had a NA1, great cars)
For me 09 egear vs 06 egear is not too much of difference in terms of price, but if it were manual 06~08 vs eGear 09+, I would take the manual over LP egear. The 09+ egear LPs are actually great bargain ($130k to $150k).
Of course I also like latest and greatest: Huracan, new NSX, or 570s etc. I actually received Huracan trade offer for my manual LP550-2 that I turned down. As I already have plan to buy one of the newer sports car to drive as daily while always keeping at least one manual car that is considered unique and rare.
End of the day we are car enthusiast, loving and appreciate cars is what we do.