Recently I noticed my front brakes are incredibly  weak after riding a friends R3. My bike  is a 2007, 15k miles, I  changed  the front pads with EBC organic pads and did a brake fluid flush about 5k miles, 6 months ago, the pads have plenty of material left on them. I have always felt like the front brake could be stronger, but I didn’t realize how weak mine were until riding another bike. I know sport bikes will have better breaking, but it feels like my bike the front brakes are maybe 20% as strong. On that bike I almost has ABS kicking in when I pulled the brake lever with 50% of my strength. On my bike I need to squeeze with about 70% of my strength to get any form of braking at all.

Could this be an issue with the rubber front brake line being old and worn out and I should replace it? I have tried holding the brake line and then squeezing the lever as hard as I can to check for any expansion/swelling. It maybe expanded a very very tiny amount but not enough for me to think it’s the problem and needs to be replaced. I don’t think there are any air bubbles in the line, I can pull the brake lever about 20% of the way to the handlebar and after that it doesn’t move anymore with any additional pressure.

Any thought or fixes to improve the strength of the front brakes?

I believe the front brake on the Savage was intentionally made to be a bit "soft" - to allow beginner riders some room for error.

I have bumped the Big Brake kit to the top of the list in the Marketplace - I am not sure if they are still available......if you are interested you will have to contact him and see.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1475013866/0

If you are handy at fabricating pieces - a left side brake caliper from a Suzuki SV650 can be adapted to fit......and it makes for a very strong front brake.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1506653047/11#11

I went with an HEL stainless braided line, super easy plug and play and reasonable prices and colour choices.  Made a huge difference in feel to me (though mine is much older than yours)

https://us.helperformance.com/

I find the front break better then on my old bikes.
But those bikes was 25 years ago.. double levers drum brakes in the front.
In any case, you have alredy noticed that there is a lot of nasty looking stuff.. get rid of that in the first place.

IE, make it to at least original!

To that.. I dont think that enginers at Suzuki dont solved the problem of getting  a functional front brake?

And to that.. there are still some extra other suppliers of parts to our bike.

In anyway, there are probably no issues to get those parts frome other suppliers, like the Stainles braided  lines?

But at first.. get rid of all any isuies!