So for this fanfiction, I have made some changes which I will base on my belief. So if they are wrong or something doesn't match, you can correct me, but it will probably stay the same as I have a plan why I did it like this. It is related to obtaining the Rinnegan and the jutsu "Izanagi".
1. Izanagi is too broken so I nerfed it. To activate this jutsu, you have to be a member of the Uchiha clan or have Hashirama cells in your body.
2. Using it costs a normal Sharingan, as shown in the fight 'Obito vs. Konan', which goes blind( here it only goes white) AND part of your life force. (you basically grow weak during the use).
The reason for Madara waiting so long to get the Rinnegan is simple. In this fanfiction, he fought Hashirama when he was like 40~50 years old and used a full delayed eternal mangekyō Sharingan to come back to life. This cost him some life force. Then he basically went into hiding.
No "zenkai boost" as he doesn't fight anymore and waits like a 'female cat'. At some point, like 15~20 years, he finally awakens the Rinnegan restoring his Sharingan.
Now he is like 60~70 years. This dude is old as a modern human in a ninja world. Summoning the Gedo Mazo he goes on life support and waits for an Uchiha he can brainwash to do his biddings after he finally goes into his grave. He lives trough 3 f**** wars as he met Obito at the end of the 3rd.
Respect for Madara, he lived like 90 to 100 years. Outliving Mito Uzumaki.
Now to the main part. We have an a.d.u.l.t in his late 20s early 30s. He is strong. He has a large chakra pool for a normal Shinobi but it is not comparable with an Uzumaki, here Nagato. So using a dangerous form of chakra pool expansion Ishizu transplants the Sharingan's into his eye, making him basically blind.
Lucky for him cough "plot armor" cough he survives it as he is a descendent of the Sage.
(the same as Kinkaku and Ginkaku).
Imagine that Hagoromo had more children and from one of them Ishizu is a descendent. Now he had to expand his chakra pool using the Sharingan. Kakashi was a prime example of how not to do it as he had a Sharingan longer and went unconscious after fighting Zabuza and at that time he was like between 25 or 30(I hate to look up age so I just use my numbers).
You have to use it every time your chakra is full, using it as a muscle, but to not overdo it as it would lead you to death.
Still, Ishizu won't just acquire the Rinnegan and go full power. No, even though he knows the paths, he has to understand them. More so, it will cost him massive chakra to use just the Deva Path. If Ishizu uses a path he knows it will drain him so much chakra that he can't fight anymore. So Ishizu would probably need the time skip of 2 years to master the 6 paths and maybe get other bodies to give them each a path.
2 paths will be important here. The animal path and the 7 outer paths. Wood clones are the idea which I got my inspiration from "Yami the gamer Kage" from I'mjusttryingtofindmyway from FanFiction.Net.