Personally sillypieman, I think in your case you would be better off jumping from RPG Maker to a more advanced, easy-to-learn engine instead of just jumping in and dealing with game engine design. You completed games in RPG Maker before, something not many accomplished, so instead of going from designing games to designing engines that are cross-platform -which can become quite complex- I think it will be better for you to just expand your horizons a bit. Use a well-documented, cross-platform game engine that is easy to learn with a large helpful community. The more you use it, the more tricks you will learn which you can apply to your own engine in the future.
The engine I recommend is Unity ( http://unity3d.com/
). Unity Free can be downloaded right now and you can start working with it and learning with it. It is cross-platform, although if you want to publish for the iOS, Android, PS3, Xbox360, etc you need a license. You can publish to Windows and use the Unity Player to integrate your game into a web browser. It has a very large and helpful community which can guide you and help you solve problems.
Although you will still face all the design problems associated with programming a game from scratch, Unity will give you the tools. You will have to find ways of overcoming problems such as what you described, such as storing Items, Weapons, Enemies, etc in an easy-to-access and modify way. Luckily Unity is very versatile and you will find many user-created add-ons or plugins (Some free, others not) which may help you get started even faster.
One such package which will make the transition from RPG Maker to Unity smoother would be a RPG Development Kit (Likewise, you can find FPS Dev Kits, Racing Dev Kits, etc) which provide a solid core that you can build your game on. A solid RPG Dev Kit for Unity would be the Okashi RPG Kit ( http://rpg-kit.com/
). Basically, the Okashi RPG Kit gives you a solid base to build your game around, and provides you with editors and a data structure for databasing (Among other useful things). I think working with something like this would be the best option for you until you become more familiar with programming for games and are able to create your own data structures and solutions to many of the problems you will come across.
To summarize, slowly work your way up. Move from RPG Maker to a engine like Unity. Use a development kit to help with the transition. As you become more familiar with programming techniques and design create your own methods of databasing/whatever.