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So I don't really like the 40k rules in their entirety so I thought I would make an attempt at re-writing the core rules to an extent.
I want to scale things better and try to make it more balanced and more in keeping with the fluff (at least how I perceive it).

I'm going to work on a D12 system (not 2d6) with stats running through 0-10 and everything being roll under/equal the stat to pass (we'll find out what happens here).

There are a lot of things I will need to consider so I wanted opinions on a base line for a single marine (I'm picturing all marines as ICs in this).

I'm thinking the following.
WS 5 = 1-5 to hit
BS 5 = 1-5 to hit
S 5
T 5
W 3
I 5
A 2
LD 7
Sv 7 = 1-7 save
Cost 50 points

I'm sorry, but in this system, why are Marines significantly worse stat-wise, and significantly more expensive points-wise?

More to the point, can you explain your reasoning a little more? Right now, I'm getting the vibe of a solution looking for a problem, and I don't fully understand your reasoning for why you want to make this change. How is this more balanced (can't tell with a single sample)? How is this more in line with the fluff as you see it?

Honestly, don't bother with it - if you hate the 40k rules (which I don't blame you for, they're average at best) just play a different game with your 40k models

Warpath looks pretty mint for large scale, and Infinity is absolutely brilliant for small. Deadzone would probably also work for small. Then theres all sorts of other games popping up like Dust that could do it too

If you want to re-write the 40k rules, then re write them completely to address all the core problems.
EG the game mechanics and resolution methods do not fit the expected game play.

Or use a different rule set, as Dakkamite suggested.(Tomorrows war, Stargrunt II, Fubar etc.)

I ask for opinions for exactly the reason identified. I didn't really think the stats were quiet good enough for a standard marine.
Would you up everything by 1?

I'm trying to leave enough room for improvement without causing issues further down the line.

Also I'm just starting out with the project so there is room for adaptation and I want to do because I can. I don't believe in just accepting things they way they are.

The basic concept of a marine in this adaptation is an independent character that can be upgrades to fill any role.
Maybe a better stat line is:
WS6, BS6, S6, T6, W3, I5, A2, LD7 Sv7
A vet would be:
WS6, BS7, S6, T6, W3, I5 A3 LD8 Sv7
A captain would be:
WS7, BS7, S6, T6, W5, I6, A4 LD9 Sv9 (art armour)

Opinions?

Again, the basic math of your Marine stats is a noticeable reduction in strength in some areas, while others grow wildly out of control. Let's work this out:

Under the current system, a BS4 Marine hits on a 3+, a roughly 66% chance to hit. Under your 2d6 system, this drops to 50%.

Same goes for armor, though the reduction is only to 58%.

On the flipside, the Marine also triples the amount of wounds he has.

Why?

Right now, the numbers are inflating, creating problems that did not exist before while addressing seemingly none of them.

Well one thing to consider with a stat and Mechanic re-write is looking at units in a vacuum is never going to work.

So you have proposed marine stats.

If you wanted to have them perform statistically on the same level they do now they would be BS8 (hitting 66% of the time).

That said by using different dice you change the granularity of the system, and allow for a greater difference in skill for units.

i.e. right no a guardsman is only one step below a marine (BS 3 vs BS4). In a system like this one you could have marines at BS6, and IG at BS4 or something, which make marines relatively better vs IG than previously.

In general the system will make things less killy than they are now because unless stats are all grouping toward the top then the percentages will be worse.

I actually like using a D10 vs D12, simply because unless your goal is to make things far less killy, a D 10 allows better use of lower stats without penalizing them quite as much.

D12 is an odd dice. I suggest you use either D6 (everyone has a bunch of these) or D10 (anyone who's played White Wolf Studios games will have a large quantity of these).

I've got a whole host of ideas for a rewrite of the 40k system, but frankly not enough time to put them all down on paper.

I will say this much, your success as far as the actual rules go hinges on using a consistent terminology. A model that is killed should always be the same status while a model that is wounded should be a distinct, separate, status on a model. Similarly, the use of terminology like "attack" or "morale" or "leadership test" should always mean the same thing and should always be affected by the same rules.
Prime example is the leadership test, which under normal 40k is vastly different depending on if it is a psychic test, an ability test or a morale test with abilities haphazardly affecting some or all with the same terminology but not necessarily the same consistency - in particular when it comes to psychic tests.

Also, do consider the style of codex and unit structure. You will most likely need help designing codexes which means you're going to need to set down rules for how to design a codex. Well, translate is maybe the better word.

Lots of excellent game use the humble D6.
There is nothing wrong with using D6 in a war game.
However, 40k has serious problems due to it being made backward compatible for game mechanics and resolution methods developed for Napoleonic warfare from the mid 1970s.

If you use modern game mechanics and resolution methods , from modern games, you can get a much better rule set, and KEEP D6s.

Eg write a rule set specificaly for 40k from scratch.(Rather than mutate and add special rule to WHFB rules.)