Squat heavy. Deadlift heavy.

That's all you need.

Two words: Cross fit. Or functional strength training. Best shape of your life, no body building necessary.

First, there's no such thing as "getting toned." Either you have muscle and it shows or you don't. Also, contrary to conventional wisdom, you really can't isolate a certain muscle and make it grow (much) bigger than the others. Granted, body builder focus on certain ones and get certain shapes, but that required LOTS of specialized work (and supplements). For normal humans with a normal gym schedule that doesn't happen.

So what do I recommend? As Trelow said, deads and squats. Basically you want to put your effort as short duration, high intensity, high weight on the biggest muscles. That will actually cause all of your muscles to grow. People often think that muscle repair from the workout is what makes them big; and, that's true to an extent. However, working out also stimulates a release of growth hormone which causes all the muscles to get big, even the ones that weren't specifically exercised. For example, look at sprinters. They do lots of heavy, explosive work with their legs and their upper bodies look great. They probably do some upper body work, but they'd be foolish if they didn't focus their time on explosive leg work; so, I bet their workouts are mostly that, and they get great upper body stimulus from that.

Granted, that doesn't mean ignore your upper body, but generally you'll want to focus on heavy, short, intense workouts that use mostly the big muscles. Compound, coordinated movements are also much better than focused, single-joint movements.

You also don't want to undo the growth hormone by doing any long, slow cardio, or even metcons. Those are actually antagonistic to muscle growth.

Look up "Starting Strength" or "Wendler 5/3/1" or my favorite "The Texas Method", those will really get you going good. Caution: don't be alarmed that it looks like very little work. Those programs have been designed and tested to work. If you add more to them, you'll just undo the benefits.

If I had to design a program it would center around

5x5 or 5x3 of Deadlifts, Squats, Power Cleans, Power Snatches, and Standing Press (only 1 or 2 of those on any given day).

Row Chest Press Pulldown Overhead Press Leg Press

You can do these exercises on machines. Your workouts should be strenuous but you shouldn't kill yourself at the gym either and give yourself plenty of rest.

Little muscle tone means you have little muscle mass, so that is what you need to get. You won't get as big as you think you would.

First off, you mention no leg exercises, and you are doing mostly single joint movements. Work in some squats, lunges, or deadlifts. They don't have to be heavy but they are very functional. Also try to do multi-joint exercises. You could do squats with dumbbells that you press at the top, so you are working legs, trunk stability and triceps/shoulders. Doing the occasional sprint intervals will help with HGH production and make both building muscle and losing weight easier, without taking a lot of time. Plus it will be a boost to your fitness abilities.

If you intend to gain strength on any level, then barbell training is the most effective way to go. If you intend to train with barbells, then you need to buy Starting Strength, learn the proper technique, and run the program through linear progression.