I really think there needs to be some kind of solution to this problem, but I don´t think lowering XP levels is the final answer for it. There is one overarching question: How do you want to connect the 2 Wastelands?
Here are 3 scenarios I could think of:
The logical (timeline) approach: The player always starts with the Fallout 3 Storyline and it there is only a one-time chance to leave DC and travel to New Vegas, which is blended over with a "4 years later" Message. Preferably this should only be possible after you finished the main story of FO3 and Broken Steel. This would somehow keep a logical timeline (as much as it is possible, since the Lone wanderer and the courier couldn´t be the same person afaik). When you arrive in New Vegas the player should get shot in the head, which leads to losing his stats. This means the players becomes level 1 again, all stats are reset and all level up perks are removed. What the player should keep are special perks (like Survival Guru, Ant Sight) a certain amount of equipment and money and some kind of bonus perk, which could be called "DC Wasteland legacy" with some bonuses (depending on how you solved FO3), that don´t make FO:NW trivial to play. Also, there would be no possibility to go back to the DC wasteland. Of course this would make some things impossible, like taking DC companions over to new Vegas and vice versa. The whole reason for doing this, is to not trivialize FO:NW, because not having all stats at 100 from the get go and leveling up is an important part of what makes the game enjoyable. This would be my preferred way of doing it, because I value having fun while playing the second story higher, than being able to do wacky stuff like using Jericho in New Vegas. This solution would keep each playthrough as near to the original experience as possible.
The universal approach: The player can either choose in which storyline he wants to start, or there is a default storyline, which allows to travel between the wastelands relatively early (like it is done at the moment). On the plus side almost everything can be done as the player wants it to be done. The problem here is, that the current leveling mechanic simply isn´t fit to handle 2 separate stories played after each other, because there are severe scaling issues, which lead to a trivial gameplay for the second story as a high level character. As you already noted there needs to be some kind of solution which allows a better scaling without making the first story too hard or still trivializing the second story. Reducing XP might be one part of a solution, but it definitely is not the final answer to the problem. But if player freedom is your vision for this mod, then this is the way to go.
The directed approach: In this approach the player should be able to choose his starting storyline. The first story the player chooses should have a level cap, so that you have a level value to balance the second story around. When the first story is finished, the player can start the second story, and everything in the second story needs to scale up to be a challenge for the high level player. In this case you might allow travel between the 2 wastelands after the first one is finished. Essentially the max level of the first story is the equivalent of a level 1 character in the second story. I guess this would be a lot of work, since there are so many things that you need to scale (skill checks, Enemies, loot, prices, perks, SPECIAL stats, skill stats and so on). Practical I think his approach wouldn´t be feasible, since it´s just too much work.
These are the 3 general ways I could see your mod implemented, but of course there could be some in between solutions or even some others I didn´t think of. Currently I think you are going for number 2, and I guess it´s a tough call to change it. I´ll wrap my head around for some sort of solution, but I think the whole leveling system might need a rework if you want this to work out with free traveling.
) but what comes into mind is something like "More Perks".
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