I respect that you enjoy the show and I'm glad it works for you. This is why it doesn't work for most of us
The producers made it clear from Day One that they were going their own way and throwing in references whenever they felt like it, without sticking too close to comic canon.
This is the thing. The reason most people hate Gotham is because they went their own way. They had a wealth of source material to work from and more than enough wiggle room for creative changes, but they chose to outright ignore all of it.
If they changed character names, this would be a perfectly servicable middle-of-the-road cop drama, but because it has DC characters in it, it suddenly needs to be held accountable as if it's some sort of official Year One interpretation.
You're right. If the characters had different names I'd probly think it was an ok cop drama. But that's the problem. Because they ARE making a DC show there are certain things that have to happen certain ways. Those characters have rules. There are certain things that can not change when you make an adaptation, like the ages of all of the characters for example. Harvey Bullock should be younger than Jim Gordon. Harvey Dent and Edward Nygma should be just as old as Bruce. Carmine Falcone shouldn't be 1000 already. The show doesn't feel right because the characters aren't right.
The biggest problem is the characters as a whole. They can't grow or change, really at all, because they already behave and have the personalities/quirks of their older selves. For example, Selina Kyle is already a master burglar, runs around on rooftops in a leather outfit, and is completely cat obsessed. We see all of this within the first 5 minutes of the pilot. Edward Nygma's FIRST LINE OF DIALOGUE is an obscure riddle. In episode 2, Bruce is talking about conquering his fear and overcoming pain. They're doing the joker already, and from what we've seen he's basically already the clown prince of crime sans the green hair and albino skin tone. They don't trust their audience to be able to discern for themselves who these characters are going to grow up to be. They think you're stupid.
In conclusion: when there is almost a century of source material to work from, work from it. It will make for a better show. Don't make creative changes to your characters for the purpose of "Easter eggs." Easter eggs are fun, but they can't, won't, and shouldn't be expected to hold up the show. And finally, don't insult our intelligence by completely abandoning subtlety and character development.